Propionyl-CoA carboxylase

Propionyl-CoA carboxylase
Identifiers
EC number 6.4.1.3
CAS number 9023-94-3
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Methylmalonyl-CoA decarboxylase
Identifiers
EC number 4.1.1.41
CAS number 37289-44-4
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

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 + propanoyl-CoA + HCO3- <=> ADP + phosphate + (S)-methylmalonyl-CoA

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

Contents

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]

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.

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. [6] The N1 of biotin is thought to be the active site base.[7]

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. [8] 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.[9] Later (2004), it was suggested that Arginine-338 serves to orient the carboxyphosphate intermediate for optimal carboxylation of biotin. [10]

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.[11] With biotin, optimum pH is 8.0-8.5.[12]

Enzyme Mechanism

The normal catalytic reaction mechanism involves a carbanion intermediate and does not proceed through a concerted process.[13] Figure 3 shows a probable pathway.

The reaction has been shown to be slightly reversible at low propionyl-CoA flux.[14]

Isozymes

Humans express the following two propionyl-CoA carboxylase isozymes:

propionyl Coenzyme A carboxylase, alpha polypeptide
Identifiers
Symbol PCCA
Entrez 5095
HUGO 8653
OMIM 232000
RefSeq NM_000282
UniProt P05165
Other data
EC number 6.4.1.3
Locus Chr. 13 q32
propionyl Coenzyme A carboxylase, beta polypeptide
Identifiers
Symbol PCCB
Entrez 5096
HUGO 8654
OMIM 232050
RefSeq NM_000532
UniProt P05166
Other data
EC number 6.4.1.3
Locus Chr. 3 q21-q22

Pathology

A deficiency is associated with propionic acidemia.[15][16][17]

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.[18]

Regulation

Of Propionyl-CoA Carboxylase

a. Carbamazepine (antiepileptic drug): significantly lowers enzyme levels in the liver[19]

b. E. coli chaperonin proteins groES and groEL: essential for folding and assembly of human PCC heteromeric subunits[20]

c. Bicarbonate: negative cooperativity[21]

d. Mg2+ and MgATP2-: allosteric activation[22]

By Propionyl-CoA Carboxylase

a. 6-Deoxyerythronolide B: decrease in PCC levels lead to increased production [23]

b. Glucokinase in pancreatic beta cells: precursor of beta-PCC shown to decrease KM and increase Vmax; activation [24]

See also

References

  1. ^ EC 6.4.1.3
  2. ^ EC 4.1.1.41
  3. ^ Kalousek F, Darigo MD, Rosenberg LE. Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of nonidentical subunits. J Biol Chem. 1980 Jan 10;255(1):60-5. PMID 6765947
  4. ^ Diacovich L, Mitchell DL, Pham H, Gago G, Melgar MM, Khosla C, Gramajo H, Tsai SC. Crystal structure of the beta-subunit of acyl-CoA carboxylase: structure-based engineering of substrate specificity. Biochemistry. 2004 Nov 9;43(44):14027-36. PMID 15518551
  5. ^ a b c Huang CS, Sadre-Bazzaz K, Shen Y, Deng B, Zhou ZH, Tong L. Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase. Nature. 2010 Aug 19;466(7309):1001-5. PMID 20725044; Full text at PMC: 2925307
  6. ^ Kalousek F, Darigo MD, Rosenberg LE. Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of nonidentical subunits. J Biol Chem. 1980 Jan 10;255(1):60-5. PMID 6765947
  7. ^ Diacovich L, Mitchell DL, Pham H, Gago G, Melgar MM, Khosla C, Gramajo H, Tsai SC. Crystal structure of the beta-subunit of acyl-CoA carboxylase: structure-based engineering of substrate specificity. Biochemistry. 2004 Nov 9;43(44):14027-36. PMID 15518551
  8. ^ Arabolaza A, Shillito ME, Lin TW, Diacovich L, Melgar M, Pham H, Amick D, Gramajo H, Tsai SC. Crystal structures and mutational analyses of acyl-CoA carboxylase beta subunit of Streptomyces coelicolor. Biochemistry. 2010 Aug 31;49(34):7367-76. PMID 20690600; Full text at PMC: 2927733
  9. ^ Wolf B, Kalousek F, Rosenberg LE. Essential arginine residues in the active sites of propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase. Enzyme. 1979;24(5):302-6. PMID 510274
  10. ^ Sloane V, Waldrop GL. Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria: evidence for cooperativity in biotin carboxylase. J Biol Chem. 2004 Apr 16;279(16):15772-8. Epub 2004 Feb 11. PMID 14960587
  11. ^ Kalousek F, Darigo MD, Rosenberg LE. Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of nonidentical subunits. J Biol Chem. 1980 Jan 10;255(1):60-5. PMID 6765947
  12. ^ Hsia YE, Scully KJ, Rosenberg LE. Human propionyl CoA carboxylase: some properties of the partially purified enzyme in fibroblasts from controls and patients with propionic acidemia. Pediatr Res. 1979 Jun;13(6):746-51. PMID 481943
  13. ^ Stubbe J, Fish S, Abeles RH. Are carboxylations involving biotin concerted or nonconcerted? J Biol Chem. 1980 Jan 10;255(1):236-42. PMID 7350155
  14. ^ Reszko AE, Kasumov T, Pierce BA, David F, Hoppel CL, Stanley WC, Des Rosiers C, Brunengraber H. Assessing the reversibility of the anaplerotic reactions of the propionyl-CoA pathway in heart and liver. J Biol Chem. 2003 Sep 12;278(37):34959-65. Epub 2003 Jun 24. PMID 12824185
  15. ^ Ugarte M, Pérez-Cerdá C, Rodríguez-Pombo P, Desviat LR, Pérez B, Richard E, Muro S, Campeau E, Ohura T, Gravel RA (1999). "Overview of mutations in the PCCA and PCCB genes causing propionic acidemia". Hum. Mutat. 14 (4): 275–82. doi:10.1002/(SICI)1098-1004(199910)14:4<275::AID-HUMU1>3.0.CO;2-N. PMID 10502773. 
  16. ^ 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". Mol. Genet. Metab. 83 (1-2): 28–37. doi:10.1016/j.ymgme.2004.08.001. PMID 15464417. 
  17. ^ Deodato F, Boenzi S, Santorelli FM, Dionisi-Vici C (May 2006). "Methylmalonic and propionic aciduria". Am J Med Genet C Semin Med Genet 142C (2): 104–12. doi:10.1002/ajmg.c.30090. PMID 16602092. 
  18. ^ Stratton SL, Bogusiewicz A, Mock MM, Mock NI, Wells AM, Mock DM. Lymphocyte propionyl-CoA carboxylase and its activation by biotin are sensitive indicators of marginal biotin deficiency in humans. Am J Clin Nutr. 2006 Aug;84(2):384-8. PMID 16895887; Full text at PMC: 1539098
  19. ^ Rathman SC, Eisenschenk S, McMahon RJ. The abundance and function of biotin-dependent enzymes are reduced in rats chronically administered carbamazepine. J Nutr. 2002 Nov;132(11):3405-10. PMID 12421859
  20. ^ Kelson TL, Ohura T, Kraus JP. Chaperonin-mediated assembly of wild-type and mutant subunits of human propionyl-CoA carboxylase expressed in Escherichia coli. Hum Mol Genet. 1996 Mar;5(3):331-7. PMID 8852656
  21. ^ Sloane V, Waldrop GL. Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria: evidence for cooperativity in biotin carboxylase. J Biol Chem. 2004 Apr 16;279(16):15772-8. Epub 2004 Feb 11. PMID 14960587
  22. ^ McKeon C, Wolf B. Magnesium and magnesium adenosine triphosphate activation of human propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase. Enzyme. 1982;28(1):76-81. PMID 6981505
  23. ^ Zhang H, Boghigian BA, Pfeifer BA. Investigating the role of native propionyl-CoA and methylmalonyl-CoA metabolism on heterologous polyketide production in Escherichia coli. Biotechnol Bioeng. 2010 Feb 15;105(3):567-73. PMID 19806677
  24. ^ Shiraishi A, Yamada Y, Tsuura Y, Fijimoto S, Tsukiyama K, Mukai E, Toyoda Y, Miwa I, Seino Y. A novel glucokinase regulator in pancreatic beta cells: precursor of propionyl-CoA carboxylase beta subunit interacts with glucokinase and augments its activity. J Biol Chem. 2001 Jan 26;276(4):2325-8. Epub 2000 Nov 20. PMID 11085976

External links

Ligases: carbon-carbon ligases (EC 6.4)
Biotin dependent carboxylase
Other
B enzm: 1.1/2/3/4/5/6/7/8/10/11/13/14/15-18, 2.1/2/3/4/5/6/7/8, 2.7.10, 2.7.11-12, 3.1/2/3/4/5/6/7, 3.1.3.48, 3.4.21/22/23/24, 4.1/2/3/4/5/6, 5.1/2/3/4/99, 6.1-3/4/5-6
Synthesis
Malonyl-CoA synthesis
Fatty acid desaturases
Triacyl glycerol
Degradation
General
Propionyl-CoA carboxylase
Other

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m(A16/C10),i(k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)
K→acetyl-CoA
(see below)
G
Other
→succinyl-CoA→TCA
Propionyl-CoA carboxylase · Methylmalonyl CoA epimerase · Methylmalonyl-CoA mutase

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m(A16/C10),i(k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)