Jump to content

Propionyl-CoA carboxylase

From Wikipedia, the free encyclopedia

This is an old revision of this page, as edited by Leyo (talk | contribs) at 22:21, 11 February 2015 (correct minus sign in superscript). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

Propionyl-CoA carboxylase
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
Methylmalonyl-CoA decarboxylase
Identifiers
EC no.4.1.1.41
CAS no.37289-44-4
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 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 B12-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 + HCO3− <=> ADP + phosphate + (S)-methylmalonyl-CoA

It has been classified both as a ligase[1] and a lyase.[2]

Enzyme Structure

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]

Enzyme Mechanism

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]

Isozymes

Humans express the following two propionyl-CoA carboxylase isozymes:

propionyl Coenzyme A carboxylase, alpha polypeptide
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
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

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]

Regulation

Of Propionyl-CoA Carboxylase

a. Carbamazepine (antiepileptic drug): significantly lowers enzyme levels in the liver[16]

b. E. coli chaperonin proteins groES and groEL: essential for folding and assembly of human PCC heteromeric subunits[17]

c. Bicarbonate: negative cooperativity[8]

d. Mg2+ and MgATP2−: allosteric activation[18]

By Propionyl-CoA Carboxylase

a. 6-Deoxyerythronolide B: decrease in PCC levels lead to increased production [19]

b. Glucokinase in pancreatic beta cells: precursor of beta-PCC shown to decrease KM and increase Vmax; activation [20]

See also

References

  1. ^ EC 6.4.1.3
  2. ^ EC 4.1.1.41
  3. ^ a b c Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 6765947, please use {{cite journal}} with |pmid=6765947 instead.
  4. ^ a b Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 15518551, please use {{cite journal}} with |pmid=15518551 instead.
  5. ^ a b c Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 20725044, please use {{cite journal}} with |pmid=20725044 instead.
  6. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 20690600, please use {{cite journal}} with |pmid=20690600 instead.
  7. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 510274, please use {{cite journal}} with |pmid=510274 instead.
  8. ^ a b Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 14960587, please use {{cite journal}} with |pmid=14960587 instead.
  9. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 481943, please use {{cite journal}} with |pmid=481943 instead.
  10. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 7350155, please use {{cite journal}} with |pmid=7350155 instead.
  11. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 12824185, please use {{cite journal}} with |pmid=12824185 instead.
  12. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 10502773, please use {{cite journal}} with |pmid=10502773 instead.
  13. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 15464417, please use {{cite journal}} with |pmid=15464417 instead.
  14. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 16602092 , please use {{cite journal}} with |pmid=16602092 instead.
  15. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 16895887, please use {{cite journal}} with |pmid=16895887 instead.
  16. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 12421859, please use {{cite journal}} with |pmid=12421859 instead.
  17. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 8852656, please use {{cite journal}} with |pmid=8852656 instead.
  18. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 6981505, please use {{cite journal}} with |pmid=6981505 instead.
  19. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 19806677, please use {{cite journal}} with |pmid=19806677 instead.
  20. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 11085976, please use {{cite journal}} with |pmid=11085976 instead.
Retrieved from "https://en.wikipedia.org/w/index.php?title=Propionyl-CoA_carboxylase&oldid=646710566"