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{{enzyme
{{infobox enzyme
| Name = Propionyl-CoA carboxylase
| Name = Propionyl-CoA carboxylase
| EC_number = 6.4.1.3
| EC_number = 6.4.1.3
| CAS_number = 9023-94-3
| CAS_number = 9023-94-3
⚫
| GO_code = 0004658
| IUBMB_EC_number = 6/4/1/3
| GO_code = 0004658
| image = 6ybp.jpg
| image =
| width = 270
| caption = Propionyl-CoA carboxylase hetero12mer, Methylorubrum extorquens
| width =
| caption =
}}
{{enzyme
| Name = Methylmalonyl-CoA decarboxylase
| EC_number = 4.1.1.41
| CAS_number = 37289-44-4
| IUBMB_EC_number = 4/1/1/41
⚫
| GO_code = 0004492
| image =
| width =
| caption =
}}
}}


'''Propionyl-CoA carboxylase''' ({{EnzExplorer|6.4.1.3}}, '''PCC''') catalyses the [[carboxylation]] reaction of [[propionyl-CoA]] in the [[mitochondrial matrix]]. PCC has been classified both as a [[ligase]]<ref>{{EC number|6.4.1.3}}</ref> and a [[lyase]].<ref>{{EC number|4.1.1.41}}</ref> The enzyme is [[biotin]]-dependent. The product of the reaction is (S)-[[methylmalonyl CoA]].
'''Propionyl-CoA carboxylase''' catalyses the [[carboxylation]] reaction of [[propionyl CoA]] in the [[mitochondrial matrix]]. The enzyme is [[biotin]]-dependent. The product of the reaction is (S)-[[methylmalonyl CoA]]. [[Propionyl CoA]] is the end product of metabolism of odd-chain fatty acids, and is also a metabolite of most methyl-branched fatty acids. It is also the main metabolite of valine, and together with [[acetyl-CoA]], is a metabolite of isoleucine, as well as a [[methionine]] metabolite. [[Propionyl-CoA]] is thus of great importance as a [[glucose]] precursor. (S)-Methylmalonyl-CoA is not directly utilizable by animals; it is acted on by a racemase to give (R)-methylmalonyl-CoA. The latter is converted by methylmalonyl-CoA mutase (one of a very few Vitamin B<sub>12</sub>-dependent enzymes) to give [[succinyl-CoA]]. The latter is converted to [[oxaloacetate]] and then [[malate]] in the [[Krebs cycle]]. Export of [[malate]] into the cytosol leads to formation of [[oxaloacetate]], [[phosphoenol pyruvate]], and other gluconeogenic intermediates.


: ATP + propionyl-CoA + HCO<sub>3</sub><sup>−</sup> <=> ADP + phosphate + (S)-methylmalonyl-CoA
: ATP + propionyl-CoA + HCO<sub>3</sub><sup>−</sup> <=> ADP + phosphate + (S)-methylmalonyl-CoA


(S)-Methylmalonyl-CoA cannot be directly utilized by animals. It is acted upon by a [[racemase]], yielding (R)-methylmalonyl-CoA, which is then converted into [[succinyl-CoA]] by methylmalonyl-CoA mutase (one of the few metabolic enzymes which requires [[vitamin B12]] as a cofactor). Succinyl-CoA, a [[Krebs cycle]] intermediate, is further metabolized into [[fumarate]], then [[malate]], and then [[oxaloacetate]]. Oxaloacetate may be transported into the cytosol to form [[phosphoenol pyruvate]] and other gluconeogenic intermediates. Propionyl-CoA is therefore an important precursor to [[glucose]].
It has been classified both as a [[ligase]]<ref>{{EC number|6.4.1.3}}</ref> and a [[lyase]].<ref>{{EC number|4.1.1.41}}</ref>

Propionyl-CoA is the end product of odd-chain fatty acid metabolism, including most methylated [[fatty acid]]s. The amino acids [[valine]], [[isoleucine]], and [[methionine]] are also substrates for propionyl-CoA metabolism.


==Enzyme Structure==
== Structure ==


Propionyl-CoA Carboxylase (PCC) is a 750 kDa alpha(6)-beta(6)-dodecamer. (Only approximately 540 kDa is native enzyme. <ref name="PubMedCitation">{{Cite pmid|6765947|noedit}}</ref> ) The alpha subunits are arranged as monomers, decorating the central beta-6 hexameric core. Said core is oriented as a short cylinder with a hole along its axis.
Propionyl-CoA carboxylase (PCC) is a 750 kDa alpha(6)-beta(6)-dodecamer. (Only approximately 540 kDa is native enzyme.<ref name="PubMedCitation">{{cite journal | vauthors = Kalousek F, Darigo MD, Rosenberg LE | title = Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of nonidentical subunits | journal = The Journal of Biological Chemistry | volume = 255 | issue = 1 | pages = 60–65 | date = January 1980 | doi = 10.1016/S0021-9258(19)86263-4 | pmid = 6765947 | doi-access = free }}</ref> ) The alpha subunits are arranged as monomers, decorating the central beta-6 hexameric core. Said core is oriented as a short cylinder with a hole along its axis.
The alpha subunit of PCC contains the [[biotin carboxylase]] (BC) and [[biotin]] carboxyl carrier protein (BCCP) domains. A domain known as the BT domain is also located on the alpha subunit and is essential for interactions with the beta subunit. The 8-stranded anti-parallel [[beta barrel]] fold of this domain is particularly interesting. The beta subunit contains the carboxyltransferase (CT) activity.<ref name="diacovich">{{Cite pmid|15518551|noedit}}</ref>
The alpha subunit of PCC contains the [[biotin carboxylase]] (BC) and [[biotin carboxyl carrier protein]] (BCCP) domains. A domain known as the BT domain is also located on the alpha subunit and is essential for interactions with the beta subunit. The 8-stranded anti-parallel [[beta barrel]] fold of this domain is particularly interesting. The beta subunit contains the carboxyltransferase (CT) activity.<ref name="diacovich">{{cite journal | vauthors = Diacovich L, Mitchell DL, Pham H, Gago G, Melgar MM, Khosla C, Gramajo H, Tsai SC | display-authors = 6 | title = Crystal structure of the beta-subunit of acyl-CoA carboxylase: structure-based engineering of substrate specificity | journal = Biochemistry | volume = 43 | issue = 44 | pages = 14027–14036 | date = November 2004 | pmid = 15518551 | pmc = | doi = 10.1021/bi049065v }}</ref>


[[File:Nihms213291f1.jpg|left|thumb|Figure 1.(a). Schematic drawing of the structure of the RpPCCα-RdPCCβ chimera, viewed down the three-fold symmetry axis. Domains in the α and β subunits in the top half of the structure are given different colors, and those in the first α and β subunits are labeled. The α and β subunits in the bottom half are colored in magenta and green, respectively. The red arrow indicates the viewing direction of panel b. (b). Structure of the RpPCCα-RdPCCβ chimera, viewed down the two-fold symmetry axis. The red rectangle indicates the region shown in detail in Fig. 2a. (c). Cryo-EM reconstruction of HsPCC at 15 Å resolution, viewed in the same orientation as panel a. The atomic model of the chimera was fit into the cryo-EM envelope. (d). The cryo-EM reconstruction viewed in the same orientation as panel b. The arrows indicate a change in the BCCP position that is needed to fit the cryo-EM map. All the structure figures were produced with PyMOL (www.pymol.org), and the cryo-EM figures were produced with Chimera.<ref name="huang">{{Cite pmid|20725044|noedit}}</ref> This provides clear evidence of crucial dimeric interaction between alpha and beta subunits.]]
[[File:Nihms213291f1.jpg|left|thumb|Figure 1.(a). Schematic drawing of the structure of the RpPCCα-RdPCCβ chimera, viewed down the three-fold symmetry axis. Domains in the α and β subunits in the top half of the structure are given different colors, and those in the first α and β subunits are labeled. The α and β subunits in the bottom half are colored in magenta and green, respectively. The red arrow indicates the viewing direction of panel b. (b). Structure of the RpPCCα-RdPCCβ chimera, viewed down the two-fold symmetry axis. The red rectangle indicates the region shown in detail in Fig. 2a. (c). Cryo-EM reconstruction of HsPCC at 15 Å resolution, viewed in the same orientation as panel a. The atomic model of the chimera was fit into the cryo-EM envelope. (d). The cryo-EM reconstruction viewed in the same orientation as panel b. The arrows indicate a change in the BCCP position that is needed to fit the cryo-EM map. All the structure figures were produced with PyMOL (www.pymol.org), and the cryo-EM figures were produced with Chimera.<ref name="huang">{{cite journal | vauthors = Huang CS, Sadre-Bazzaz K, Shen Y, Deng B, Zhou ZH, Tong L | title = Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase | journal = Nature | volume = 466 | issue = 7309 | pages = 1001–1005 | date = August 2010 | pmid = 20725044 | pmc = 2925307 | doi = 10.1038/nature09302 }}</ref> This provides clear evidence of crucial dimeric interaction between alpha and beta subunits.]]


The BC and CT sites are approximately 55 Å apart, indicative of the entire BCCP domain translocating during catalysis of the [[carboxylation]] of [[propionyl-CoA]]. <ref name =huang /> This provides clear evidence of crucial dimeric interaction between alpha and beta subunits.
The BC and CT sites are approximately 55 Å apart, indicative of the entire BCCP domain translocating during catalysis of the [[carboxylation]] of [[propionyl-CoA]].<ref name =huang /> This provides clear evidence of crucial dimeric interaction between alpha and beta subunits.


[[File:Nihms213291f3.jpg|thumb|Figure 2.(a). Schematic drawing of the relative positioning of the BC and CT active sites in the holoenzyme. One α subunit and a β2 dimer (β1 from one layer and β4 from the other layer) are shown, and the viewing direction is the same as Fig. 1b. The two active sites are indicated with the stars, separated by 55 Å distance. The bound positions of ADP in complex with E. coli BC 18 and that of CoA in complex with the 12S subunit of transcarboxylase 21 are also shown. (b). Detailed interactions between BCCP-biotin and the C domain of a β subunit. Hydrogen-bonding interactions are indicated with the dashed lines in red. The N1′ atom of biotin is labeled as 1′, hydrogen-bonded to the main-chain carbonyl of Phe397. (c). Molecular surface of the CT active site, showing a deep canyon where both substrates are bound. (d). Schematic drawing of the CT active site.<ref name =huang />]]
[[File:Nihms213291f3.jpg|thumb|Figure 2.(a). Schematic drawing of the relative positioning of the BC and CT active sites in the holoenzyme. One α subunit and a β2 dimer (β1 from one layer and β4 from the other layer) are shown, and the viewing direction is the same as Fig. 1b. The two active sites are indicated with the stars, separated by 55 Å distance. The bound positions of ADP in complex with E. coli BC 18 and that of CoA in complex with the 12S subunit of transcarboxylase 21 are also shown. (b). Detailed interactions between BCCP-biotin and the C domain of a β subunit. Hydrogen-bonding interactions are indicated with the dashed lines in red. The N1′ atom of biotin is labeled as 1′, hydrogen-bonded to the main-chain carbonyl of Phe397. (c). Molecular surface of the CT active site, showing a deep canyon where both substrates are bound. (d). Schematic drawing of the CT active site.<ref name =huang />]]


The biotin-binding pocket of PCC is hydrophobic and highly conserved. Biotin and propionyl-CoA bind perpendicular to each other in the [[oxyanion hole]]-containing active site. The native enzyme to biotin ratio has been determined to be one mole native enzyme to 4 moles biotin. <ref name="PubMedCitation" /> The N1 of biotin is thought to be the active site base.<ref name="diacovich" />
The biotin-binding pocket of PCC is hydrophobic and highly conserved. Biotin and propionyl-CoA bind perpendicular to each other in the [[oxyanion hole]]-containing active site. The native enzyme to biotin ratio has been determined to be one mole native enzyme to 4 moles biotin.<ref name="PubMedCitation" /> The N1 of biotin is thought to be the active site base.<ref name="diacovich" />


[[Site-directed mutagenesis]] at D422 shows a change in the substrate specificity of the propionyl-CoA binding site, thus indicating this residue’s importance in PCC’s catalytic activity. <ref>{{Cite pmid|20690600|noedit}}</ref> In 1979, inhibition by [[phenylglyoxal]] determined that a phosphate group from either propionyl-CoA or [[Adenosine triphosphate|ATP]] reacts with an essential arginine residue in the active site during catalysis.<ref>{{Cite pmid|510274|noedit}}</ref> Later (2004), it was suggested that Arginine-338 serves to orient the carboxyphosphate intermediate for optimal carboxylation of biotin. <ref name="PubMedCitation_a">{{Cite pmid|14960587|noedit}}</ref>
[[Site-directed mutagenesis]] at D422 shows a change in the substrate specificity of the propionyl-CoA binding site, thus indicating this residue's importance in PCC's catalytic activity.<ref>{{cite journal | vauthors = Arabolaza A, Shillito ME, Lin TW, Diacovich L, Melgar M, Pham H, Amick D, Gramajo H, Tsai SC | display-authors = 6 | title = Crystal structures and mutational analyses of acyl-CoA carboxylase beta subunit of Streptomyces coelicolor | journal = Biochemistry | volume = 49 | issue = 34 | pages = 7367–7376 | date = August 2010 | pmid = 20690600 | pmc = 2927733 | doi = 10.1021/bi1005305 }}</ref> In 1979, inhibition by [[phenylglyoxal]] determined that a phosphate group from either propionyl-CoA or [[Adenosine triphosphate|ATP]] reacts with an essential arginine residue in the active site during catalysis.<ref>{{cite journal | vauthors = Wolf B, Kalousek F, Rosenberg LE | title = Essential arginine residues in the active sites of propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase | journal = Enzyme | volume = 24 | issue = 5 | pages = 302–306 | year = 1979 | pmid = 510274 | doi = 10.1159/000458679 }}</ref> Later (2004), it was suggested that Arginine-338 serves to orient the carboxyphosphate intermediate for optimal carboxylation of biotin.<ref name="PubMedCitation_a">{{cite journal | vauthors = Sloane V, Waldrop GL | title = Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria: evidence for cooperativity in biotin carboxylase | journal = The Journal of Biological Chemistry | volume = 279 | issue = 16 | pages = 15772–15778 | date = April 2004 | pmid = 14960587 | pmc = | doi = 10.1074/jbc.M311982200 | doi-access = free }}</ref>


The [[Michaelis–Menten kinetics|KM]] values for ATP, propionyl-CoA, and bicarbonate has been determined to be 0.08 mM, 0.29 mM, and 3.0 mM, respectively. The [[isoelectric point]] falls at pH 5.5. PCC’s structural integrity is conserved over the temperature range of -50 to 37 degrees Celsius and the pH range of 6.2 to 8.8. Optimum pH was shown to be between 7.2 and 8.8 without biotin bound.<ref name="PubMedCitation" /> With biotin, optimum pH is 8.0-8.5.<ref>{{Cite pmid|481943|noedit}}</ref>
The [[Michaelis–Menten kinetics|KM]] values for ATP, propionyl-CoA, and bicarbonate has been determined to be 0.08 mM, 0.29 mM, and 3.0 mM, respectively. The [[isoelectric point]] falls at pH 5.5. PCC's structural integrity is conserved over the temperature range of -50 to 37 degrees Celsius and the pH range of 6.2 to 8.8. Optimum pH was shown to be between 7.2 and 8.8 without biotin bound.<ref name="PubMedCitation" /> With biotin, optimum pH is 8.0-8.5.<ref>{{cite journal | vauthors = Hsia YE, Scully KJ, Rosenberg LE | title = Human propionyl CoA carboxylase: some properties of the partially purified enzyme in fibroblasts from controls and patients with propionic acidemia | journal = Pediatric Research | volume = 13 | issue = 6 | pages = 746–751 | date = June 1979 | pmid = 481943 | doi = 10.1203/00006450-197906000-00005 | doi-access = free }}</ref>


==Enzyme Mechanism==
== Mechanism ==


The normal catalytic reaction mechanism involves a [[carbanion]] intermediate and does not proceed through a concerted process.<ref>{{Cite pmid|7350155|noedit}}</ref> Figure 3 shows a probable pathway.
The normal catalytic reaction mechanism involves a [[carbanion]] intermediate and does not proceed through a concerted process.<ref>{{cite journal | vauthors = Stubbe J, Fish S, Abeles RH | title = Are carboxylations involving biotin concerted or nonconcerted? | journal = The Journal of Biological Chemistry | volume = 255 | issue = 1 | pages = 236–242 | date = January 1980 | doi = 10.1016/S0021-9258(19)86289-0 | pmid = 7350155 | doi-access = free }}</ref> Figure 3 shows a probable pathway.


[[File:Labeled PCC Mechanism.pdf|thumb|Figure 3. Probable PCC Mechanism]]
[[File:Labeled PCC Mechanism.pdf|thumb|Figure 3. Probable PCC Mechanism]]


The reaction has been shown to be slightly reversible at low propionyl-CoA flux.<ref>{{cite journal | vauthors = Reszko AE, Kasumov T, Pierce BA, David F, Hoppel CL, Stanley WC, Des Rosiers C, Brunengraber H | display-authors = 6 | title = Assessing the reversibility of the anaplerotic reactions of the propionyl-CoA pathway in heart and liver | journal = The Journal of Biological Chemistry | volume = 278 | issue = 37 | pages = 34959–34965 | date = September 2003 | pmid = 12824185 | pmc = | doi = 10.1074/jbc.M302013200 | doi-access = free }}</ref>
The reaction has been shown to be slightly reversible at low propionyl-CoA flux.<ref>{{Cite pmid|12824185|noedit}}</ref>


== Isozymes ==
== Subunit genes ==
Human propionyl-CoA carboxylase contains two subunits, each encoded by a separate gene:
Humans express the following two propionyl-CoA carboxylase [[isozyme]]s:
{|
{|
|{{protein
|{{infobox protein
|Name=propionyl Coenzyme A carboxylase, alpha polypeptide
|Name=propionyl Coenzyme A carboxylase, alpha polypeptide
|caption= Propionyl-CoA carboxylase A homo6mer, Methylorubrum extorquens
|caption=
|image=
|image= 6ybpa.jpg
|width=
|width= 270
|HGNCid=8653
|HGNCid=8653
|Symbol=PCCA
|Symbol=PCCA
Line 74: Line 65:
|LocusSupplementaryData=
|LocusSupplementaryData=
}}
}}
|{{protein
|{{infobox protein
|Name=propionyl Coenzyme A carboxylase, beta polypeptide
|Name=propionyl Coenzyme A carboxylase, beta polypeptide
|caption= Propionyl-CoA carboxylase B homo6mer, Methylorubrum extorquens
|caption=
|image=
|image= 6ybpb.jpg
|width=
|width= 270
|HGNCid=8654
|HGNCid=8654
|Symbol=PCCB
|Symbol=PCCB
Line 95: Line 86:
|}
|}


==Pathology==
== Pathology ==
A deficiency is associated with [[propionic acidemia]].<ref name="pmid10502773">{{cite journal | vauthors = Ugarte M, Pérez-Cerdá C, Rodríguez-Pombo P, Desviat LR, Pérez B, Richard E, Muro S, Campeau E, Ohura T, Gravel RA | display-authors = 6 | title = Overview of mutations in the PCCA and PCCB genes causing propionic acidemia | journal = Human Mutation | volume = 14 | issue = 4 | pages = 275–282 | year = 1999 | pmid = 10502773 | pmc = | doi = 10.1002/(SICI)1098-1004(199910)14:4<275::AID-HUMU1>3.0.CO;2-N | s2cid = 37710112 }}</ref><ref name="pmid15464417">{{cite journal | vauthors = Desviat LR, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P, Clavero S, Ugarte M | title = Propionic acidemia: mutation update and functional and structural effects of the variant alleles | journal = Molecular Genetics and Metabolism | volume = 83 | issue = 1–2 | pages = 28–37 | year = 2004 | pmid = 15464417 | pmc = | doi = 10.1016/j.ymgme.2004.08.001 }}</ref><ref name="pmid16602092">{{cite journal | vauthors = Deodato F, Boenzi S, Santorelli FM, Dionisi-Vici C | title = Methylmalonic and propionic aciduria | journal = American Journal of Medical Genetics. Part C, Seminars in Medical Genetics | volume = 142C | issue = 2 | pages = 104–112 | date = May 2006 | pmid = 16602092 | pmc = | doi = 10.1002/ajmg.c.30090 | s2cid = 21114631 }}</ref>
A deficiency is associated with [[propionic acidemia]].<ref name="pmid10502773">{{Cite pmid|10502773|noedit}}</ref><ref name="pmid15464417">{{Cite pmid|15464417|noedit }}</ref><ref name="pmid16602092">{{Cite pmid|16602092 |noedit }}</ref>


PCC activity is the most sensitive indicator of biotin status tested to date. In future pregnancy studies, the use of lymphocyte PCC activity data should prove valuable in assessment of biotin status.<ref>{{Cite pmid|16895887|noedit}}</ref>
PCC activity is the most sensitive indicator of biotin status tested to date. In future pregnancy studies, the use of lymphocyte PCC activity data should prove valuable in assessment of biotin status.<ref>{{cite journal | vauthors = Stratton SL, Bogusiewicz A, Mock MM, Mock NI, Wells AM, Mock DM | title = Lymphocyte propionyl-CoA carboxylase and its activation by biotin are sensitive indicators of marginal biotin deficiency in humans | journal = The American Journal of Clinical Nutrition | volume = 84 | issue = 2 | pages = 384–388 | date = August 2006 | pmid = 16895887 | pmc = 1539098 | doi = 10.1093/ajcn/84.1.384 }}</ref>

===Intragenic complementation===

When multiple copies of a polypeptide encoded by a [[gene]] form an aggregate, this protein structure is referred to as a multimer. When a multimer is formed from polypeptides produced by two different [[mutant]] [[allele]]s of a particular gene, the mixed multimer may exhibit greater functional activity than the unmixed multimers formed by each of the mutants alone. In such a case, the phenomenon is referred to as [[complementation (genetics)|intragenic complementation]].

PCC is a heteropolymer composed of α and β subunits in a α<sub>6</sub>β<sub>6</sub> structure. [[Mutation]]s in PCC, either in the α subunit (PCCα) or β subunit (PCCβ) can cause [[propionic acidemia]] in humans. When different mutant skin [[fibroblast]] cell lines defective in PCCβ were fused in pairwise combinations, the β [[protein complex|heteromultimeric protein]] formed as a result often exhibited a higher level of activity than would be expected based on the activities of the parental enzymes.<ref>Rodríguez-Pombo P, Pérez-Cerdá C, Pérez B, Desviat LR, Sánchez-Pulido L, Ugarte M. Towards a model to explain the intragenic complementation in the heteromultimeric protein propionyl-CoA carboxylase. Biochim Biophys Acta. 2005;1740(3):489-498. doi:10.1016/j.bbadis.2004.10.009</ref> This finding of [[complementation (genetics)|intragenic complementation]] indicated that the multimeric structure of PCC allows cooperative interactions between the constituent PCCβ monomers that can generate a more functional form of the holoenzyme.


==Regulation==
==Regulation==


===Of Propionyl-CoA Carboxylase===
===Of Propionyl-CoA Carboxylase===
a. [[Carbamazepine]] (antiepileptic drug): significantly lowers enzyme levels in the liver<ref>{{Cite pmid|12421859|noedit}}</ref>
a. [[Carbamazepine]] (antiepileptic drug): significantly lowers enzyme levels in the liver<ref>{{cite journal | vauthors = Rathman SC, Eisenschenk S, McMahon RJ | title = The abundance and function of biotin-dependent enzymes are reduced in rats chronically administered carbamazepine | journal = The Journal of Nutrition | volume = 132 | issue = 11 | pages = 3405–3410 | date = November 2002 | pmid = 12421859 | doi = 10.1093/jn/132.11.3405 | doi-access = free }}</ref>


b. ''E. coli'' [[chaperonin]] proteins groES and groEL: essential for folding and assembly of human PCC heteromeric subunits<ref>{{Cite pmid|8852656|noedit}}</ref>
b. ''E. coli'' [[chaperonin]] proteins groES and groEL: essential for folding and assembly of human PCC heteromeric subunits<ref>{{cite journal | vauthors = Kelson TL, Ohura T, Kraus JP | title = Chaperonin-mediated assembly of wild-type and mutant subunits of human propionyl-CoA carboxylase expressed in Escherichia coli | journal = Human Molecular Genetics | volume = 5 | issue = 3 | pages = 331–337 | date = March 1996 | pmid = 8852656 | doi = 10.1093/hmg/5.3.331 | doi-access = free }}</ref>


c. Bicarbonate: negative cooperativity<ref name="PubMedCitation_a" />
c. Bicarbonate: negative cooperativity<ref name="PubMedCitation_a" />


d. Mg<sup>2+</sup> and MgATP<sup>2−</sup>: allosteric activation<ref>{{Cite pmid|6981505|noedit}}</ref>
d. Mg<sup>2+</sup> and MgATP<sup>2−</sup>: allosteric activation<ref>{{cite journal | vauthors = McKeon C, Wolf B | title = Magnesium and magnesium adenosine triphosphate activation of human propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase | journal = Enzyme | volume = 28 | issue = 1 | pages = 76–81 | year = 1982 | pmid = 6981505 | doi = 10.1159/000459088 }}</ref>


===By Propionyl-CoA Carboxylase===
===By Propionyl-CoA Carboxylase===
a. 6-Deoxyerythronolide B: decrease in PCC levels lead to increased production <ref>{{Cite pmid|19806677|noedit}}</ref>
a. 6-Deoxyerythronolide B: decrease in PCC levels lead to increased production <ref>{{cite journal | vauthors = Zhang H, Boghigian BA, Pfeifer BA | title = Investigating the role of native propionyl-CoA and methylmalonyl-CoA metabolism on heterologous polyketide production in Escherichia coli | journal = Biotechnology and Bioengineering | volume = 105 | issue = 3 | pages = 567–573 | date = February 2010 | pmid = 19806677 | pmc =9896014 | doi = 10.1002/bit.22560 | s2cid = 659042 }}</ref>


b. [[Glucokinase]] in pancreatic beta cells: precursor of beta-PCC shown to decrease KM and increase Vmax; activation <ref>{{Cite pmid|11085976|noedit}}</ref>
b. [[Glucokinase]] in pancreatic beta cells: precursor of beta-PCC shown to decrease KM and increase Vmax; activation <ref>{{cite journal | vauthors = Shiraishi A, Yamada Y, Tsuura Y, Fijimoto S, Tsukiyama K, Mukai E, Toyoda Y, Miwa I, Seino Y | display-authors = 6 | title = A novel glucokinase regulator in pancreatic beta cells: precursor of propionyl-CoA carboxylase beta subunit interacts with glucokinase and augments its activity | journal = The Journal of Biological Chemistry | volume = 276 | issue = 4 | pages = 2325–2328 | date = January 2001 | pmid = 11085976 | pmc = | doi = 10.1074/jbc.C000530200 | doi-access = free }}</ref>


==See also==
== See also ==
* [[Anaplerotic reactions]]
* [[Anaplerotic reactions]]
* [[Propionic acidemia]]
* [[Propionic acidemia]]


==References==
== References ==
{{Reflist|colwidth=35em}}
{{Reflist}}


==External links==
== External links ==
* {{MeshName|Propionyl-CoA+Carboxylase}}
* {{MeshName|Propionyl-CoA+Carboxylase}}


⚫
{{Carbon-carbon ligases}}
{{Lipid metabolism enzymes}}
{{Lipid metabolism enzymes}}
{{Amino acid metabolism enzymes}}
{{Amino acid metabolism enzymes}}
⚫
{{Carbon-carbon ligases}}
{{Enzymes}}
{{Portal bar|Biology|border=no}}

[[Category:EC 6.4.1]]
[[Category:EC 6.4.1]]
[[Category:Beta oxidation]]

Latest revision as of 19:57, 29 August 2024

Propionyl-CoA carboxylase
Propionyl-CoA carboxylase hetero12mer, Methylorubrum extorquens
Identifiers
EC no.6.4.1.3
CAS no.9023-94-3
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Search
PMCarticles
PubMedarticles
NCBIproteins

Propionyl-CoA carboxylase (EC 6.4.1.3, PCC) catalyses the carboxylation reaction of propionyl-CoA in the mitochondrial matrix. PCC has been classified both as a ligase[1] and a lyase.[2] The enzyme is biotin-dependent. The product of the reaction is (S)-methylmalonyl CoA.

ATP + propionyl-CoA + HCO3− <=> ADP + phosphate + (S)-methylmalonyl-CoA

(S)-Methylmalonyl-CoA cannot be directly utilized by animals. It is acted upon by a racemase, yielding (R)-methylmalonyl-CoA, which is then converted into succinyl-CoA by methylmalonyl-CoA mutase (one of the few metabolic enzymes which requires vitamin B12 as a cofactor). Succinyl-CoA, a Krebs cycle intermediate, is further metabolized into fumarate, then malate, and then oxaloacetate. Oxaloacetate may be transported into the cytosol to form phosphoenol pyruvate and other gluconeogenic intermediates. Propionyl-CoA is therefore an important precursor to glucose.

Propionyl-CoA is the end product of odd-chain fatty acid metabolism, including most methylated fatty acids. The amino acids valine, isoleucine, and methionine are also substrates for propionyl-CoA metabolism.

Structure

[edit]

Propionyl-CoA carboxylase (PCC) is a 750 kDa alpha(6)-beta(6)-dodecamer. (Only approximately 540 kDa is native enzyme.[3] ) The alpha subunits are arranged as monomers, decorating the central beta-6 hexameric core. Said core is oriented as a short cylinder with a hole along its axis.

The alpha subunit of PCC contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains. A domain known as the BT domain is also located on the alpha subunit and is essential for interactions with the beta subunit. The 8-stranded anti-parallel beta barrel fold of this domain is particularly interesting. The beta subunit contains the carboxyltransferase (CT) activity.[4]

Figure 1.(a). Schematic drawing of the structure of the RpPCCα-RdPCCβ chimera, viewed down the three-fold symmetry axis. Domains in the α and β subunits in the top half of the structure are given different colors, and those in the first α and β subunits are labeled. The α and β subunits in the bottom half are colored in magenta and green, respectively. The red arrow indicates the viewing direction of panel b. (b). Structure of the RpPCCα-RdPCCβ chimera, viewed down the two-fold symmetry axis. The red rectangle indicates the region shown in detail in Fig. 2a. (c). Cryo-EM reconstruction of HsPCC at 15 Å resolution, viewed in the same orientation as panel a. The atomic model of the chimera was fit into the cryo-EM envelope. (d). The cryo-EM reconstruction viewed in the same orientation as panel b. The arrows indicate a change in the BCCP position that is needed to fit the cryo-EM map. All the structure figures were produced with PyMOL (www.pymol.org), and the cryo-EM figures were produced with Chimera.[5] This provides clear evidence of crucial dimeric interaction between alpha and beta subunits.

The BC and CT sites are approximately 55 Å apart, indicative of the entire BCCP domain translocating during catalysis of the carboxylation of propionyl-CoA.[5] This provides clear evidence of crucial dimeric interaction between alpha and beta subunits.

Figure 2.(a). Schematic drawing of the relative positioning of the BC and CT active sites in the holoenzyme. One α subunit and a β2 dimer (β1 from one layer and β4 from the other layer) are shown, and the viewing direction is the same as Fig. 1b. The two active sites are indicated with the stars, separated by 55 Å distance. The bound positions of ADP in complex with E. coli BC 18 and that of CoA in complex with the 12S subunit of transcarboxylase 21 are also shown. (b). Detailed interactions between BCCP-biotin and the C domain of a β subunit. Hydrogen-bonding interactions are indicated with the dashed lines in red. The N1′ atom of biotin is labeled as 1′, hydrogen-bonded to the main-chain carbonyl of Phe397. (c). Molecular surface of the CT active site, showing a deep canyon where both substrates are bound. (d). Schematic drawing of the CT active site.[5]

The biotin-binding pocket of PCC is hydrophobic and highly conserved. Biotin and propionyl-CoA bind perpendicular to each other in the oxyanion hole-containing active site. The native enzyme to biotin ratio has been determined to be one mole native enzyme to 4 moles biotin.[3] The N1 of biotin is thought to be the active site base.[4]

Site-directed mutagenesis at D422 shows a change in the substrate specificity of the propionyl-CoA binding site, thus indicating this residue's importance in PCC's catalytic activity.[6] In 1979, inhibition by phenylglyoxal determined that a phosphate group from either propionyl-CoA or ATP reacts with an essential arginine residue in the active site during catalysis.[7] Later (2004), it was suggested that Arginine-338 serves to orient the carboxyphosphate intermediate for optimal carboxylation of biotin.[8]

The KM values for ATP, propionyl-CoA, and bicarbonate has been determined to be 0.08 mM, 0.29 mM, and 3.0 mM, respectively. The isoelectric point falls at pH 5.5. PCC's structural integrity is conserved over the temperature range of -50 to 37 degrees Celsius and the pH range of 6.2 to 8.8. Optimum pH was shown to be between 7.2 and 8.8 without biotin bound.[3] With biotin, optimum pH is 8.0-8.5.[9]

Mechanism

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The normal catalytic reaction mechanism involves a carbanion intermediate and does not proceed through a concerted process.[10] Figure 3 shows a probable pathway.

Figure 3. Probable PCC Mechanism

The reaction has been shown to be slightly reversible at low propionyl-CoA flux.[11]

Subunit genes

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Human propionyl-CoA carboxylase contains two subunits, each encoded by a separate gene:

propionyl Coenzyme A carboxylase, alpha polypeptide
Propionyl-CoA carboxylase A homo6mer, Methylorubrum extorquens
Identifiers
SymbolPCCA
NCBI gene5095
HGNC8653
OMIM232000
RefSeqNM_000282
UniProtP05165
Other data
EC number6.4.1.3
LocusChr. 13 q32
Search for
StructuresSwiss-model
DomainsInterPro
propionyl Coenzyme A carboxylase, beta polypeptide
Propionyl-CoA carboxylase B homo6mer, Methylorubrum extorquens
Identifiers
SymbolPCCB
NCBI gene5096
HGNC8654
OMIM232050
RefSeqNM_000532
UniProtP05166
Other data
EC number6.4.1.3
LocusChr. 3 q21-q22
Search for
StructuresSwiss-model
DomainsInterPro

Pathology

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A deficiency is associated with propionic acidemia.[12][13][14]

PCC activity is the most sensitive indicator of biotin status tested to date. In future pregnancy studies, the use of lymphocyte PCC activity data should prove valuable in assessment of biotin status.[15]

Intragenic complementation

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When multiple copies of a polypeptide encoded by a gene form an aggregate, this protein structure is referred to as a multimer. When a multimer is formed from polypeptides produced by two different mutant alleles of a particular gene, the mixed multimer may exhibit greater functional activity than the unmixed multimers formed by each of the mutants alone. In such a case, the phenomenon is referred to as intragenic complementation.

PCC is a heteropolymer composed of α and β subunits in a α6β6 structure. Mutations in PCC, either in the α subunit (PCCα) or β subunit (PCCβ) can cause propionic acidemia in humans. When different mutant skin fibroblast cell lines defective in PCCβ were fused in pairwise combinations, the β heteromultimeric protein formed as a result often exhibited a higher level of activity than would be expected based on the activities of the parental enzymes.[16] This finding of intragenic complementation indicated that the multimeric structure of PCC allows cooperative interactions between the constituent PCCβ monomers that can generate a more functional form of the holoenzyme.

Regulation

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Of Propionyl-CoA Carboxylase

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a. Carbamazepine (antiepileptic drug): significantly lowers enzyme levels in the liver[17]

b. E. coli chaperonin proteins groES and groEL: essential for folding and assembly of human PCC heteromeric subunits[18]

c. Bicarbonate: negative cooperativity[8]

d. Mg2+ and MgATP2−: allosteric activation[19]

By Propionyl-CoA Carboxylase

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a. 6-Deoxyerythronolide B: decrease in PCC levels lead to increased production [20]

b. Glucokinase in pancreatic beta cells: precursor of beta-PCC shown to decrease KM and increase Vmax; activation [21]

See also

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References

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  1. ^ EC 6.4.1.3
  2. ^ EC 4.1.1.41
  3. ^ a b c Kalousek F, Darigo MD, Rosenberg LE (January 1980). "Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of nonidentical subunits". The Journal of Biological Chemistry. 255 (1): 60–65. doi:10.1016/S0021-9258(19)86263-4. PMID 6765947.
  4. ^ a b Diacovich L, Mitchell DL, Pham H, Gago G, Melgar MM, Khosla C, et al. (November 2004). "Crystal structure of the beta-subunit of acyl-CoA carboxylase: structure-based engineering of substrate specificity". Biochemistry. 43 (44): 14027–14036. doi:10.1021/bi049065v. PMID 15518551.
  5. ^ a b c Huang CS, Sadre-Bazzaz K, Shen Y, Deng B, Zhou ZH, Tong L (August 2010). "Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase". Nature. 466 (7309): 1001–1005. doi:10.1038/nature09302. PMC 2925307. PMID 20725044.
  6. ^ Arabolaza A, Shillito ME, Lin TW, Diacovich L, Melgar M, Pham H, et al. (August 2010). "Crystal structures and mutational analyses of acyl-CoA carboxylase beta subunit of Streptomyces coelicolor". Biochemistry. 49 (34): 7367–7376. doi:10.1021/bi1005305. PMC 2927733. PMID 20690600.
  7. ^ Wolf B, Kalousek F, Rosenberg LE (1979). "Essential arginine residues in the active sites of propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase". Enzyme. 24 (5): 302–306. doi:10.1159/000458679. PMID 510274.
  8. ^ a b Sloane V, Waldrop GL (April 2004). "Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria: evidence for cooperativity in biotin carboxylase". The Journal of Biological Chemistry. 279 (16): 15772–15778. doi:10.1074/jbc.M311982200. PMID 14960587.
  9. ^ Hsia YE, Scully KJ, Rosenberg LE (June 1979). "Human propionyl CoA carboxylase: some properties of the partially purified enzyme in fibroblasts from controls and patients with propionic acidemia". Pediatric Research. 13 (6): 746–751. doi:10.1203/00006450-197906000-00005. PMID 481943.
  10. ^ Stubbe J, Fish S, Abeles RH (January 1980). "Are carboxylations involving biotin concerted or nonconcerted?". The Journal of Biological Chemistry. 255 (1): 236–242. doi:10.1016/S0021-9258(19)86289-0. PMID 7350155.
  11. ^ Reszko AE, Kasumov T, Pierce BA, David F, Hoppel CL, Stanley WC, et al. (September 2003). "Assessing the reversibility of the anaplerotic reactions of the propionyl-CoA pathway in heart and liver". The Journal of Biological Chemistry. 278 (37): 34959–34965. doi:10.1074/jbc.M302013200. PMID 12824185.
  12. ^ Ugarte M, Pérez-Cerdá C, Rodríguez-Pombo P, Desviat LR, Pérez B, Richard E, et al. (1999). "Overview of mutations in the PCCA and PCCB genes causing propionic acidemia". Human Mutation. 14 (4): 275–282. doi:10.1002/(SICI)1098-1004(199910)14:4<275::AID-HUMU1>3.0.CO;2-N. PMID 10502773. S2CID 37710112.
  13. ^ Desviat LR, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P, Clavero S, Ugarte M (2004). "Propionic acidemia: mutation update and functional and structural effects of the variant alleles". Molecular Genetics and Metabolism. 83 (1–2): 28–37. doi:10.1016/j.ymgme.2004.08.001. PMID 15464417.
  14. ^ Deodato F, Boenzi S, Santorelli FM, Dionisi-Vici C (May 2006). "Methylmalonic and propionic aciduria". American Journal of Medical Genetics. Part C, Seminars in Medical Genetics. 142C (2): 104–112. doi:10.1002/ajmg.c.30090. PMID 16602092. S2CID 21114631.
  15. ^ Stratton SL, Bogusiewicz A, Mock MM, Mock NI, Wells AM, Mock DM (August 2006). "Lymphocyte propionyl-CoA carboxylase and its activation by biotin are sensitive indicators of marginal biotin deficiency in humans". The American Journal of Clinical Nutrition. 84 (2): 384–388. doi:10.1093/ajcn/84.1.384. PMC 1539098. PMID 16895887.
  16. ^ Rodríguez-Pombo P, Pérez-Cerdá C, Pérez B, Desviat LR, Sánchez-Pulido L, Ugarte M. Towards a model to explain the intragenic complementation in the heteromultimeric protein propionyl-CoA carboxylase. Biochim Biophys Acta. 2005;1740(3):489-498. doi:10.1016/j.bbadis.2004.10.009
  17. ^ Rathman SC, Eisenschenk S, McMahon RJ (November 2002). "The abundance and function of biotin-dependent enzymes are reduced in rats chronically administered carbamazepine". The Journal of Nutrition. 132 (11): 3405–3410. doi:10.1093/jn/132.11.3405. PMID 12421859.
  18. ^ Kelson TL, Ohura T, Kraus JP (March 1996). "Chaperonin-mediated assembly of wild-type and mutant subunits of human propionyl-CoA carboxylase expressed in Escherichia coli". Human Molecular Genetics. 5 (3): 331–337. doi:10.1093/hmg/5.3.331. PMID 8852656.
  19. ^ McKeon C, Wolf B (1982). "Magnesium and magnesium adenosine triphosphate activation of human propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase". Enzyme. 28 (1): 76–81. doi:10.1159/000459088. PMID 6981505.
  20. ^ Zhang H, Boghigian BA, Pfeifer BA (February 2010). "Investigating the role of native propionyl-CoA and methylmalonyl-CoA metabolism on heterologous polyketide production in Escherichia coli". Biotechnology and Bioengineering. 105 (3): 567–573. doi:10.1002/bit.22560. PMC 9896014. PMID 19806677. S2CID 659042.
  21. ^ Shiraishi A, Yamada Y, Tsuura Y, Fijimoto S, Tsukiyama K, Mukai E, et al. (January 2001). "A novel glucokinase regulator in pancreatic beta cells: precursor of propionyl-CoA carboxylase beta subunit interacts with glucokinase and augments its activity". The Journal of Biological Chemistry. 276 (4): 2325–2328. doi:10.1074/jbc.C000530200. PMID 11085976.
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