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Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core.

Hall PR, Wang YF, Rivera-Hainaj RE, Zheng X, Pustai-Carey M, Carey PR, Yee VC
EMBO J 22 2334-47 (2003)
Cited: 22 times
EuropePMC logo PMID: 12743028

Abstract

Transcarboxylase from Propionibacterium shermanii is a 1.2 MDa multienzyme complex that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate, yielding propionyl-CoA and oxaloacetate. The 1.9 A resolution crystal structure of the central 12S hexameric core, which catalyzes the first carboxylation reaction, has been solved bound to its substrate methylmalonyl-CoA. Overall, the structure reveals two stacked trimers related by 2-fold symmetry, and a domain duplication in the monomer. In the active site, the labile carboxylate group of methylmalonyl-CoA is stabilized by interaction with the N-termini of two alpha-helices. The 12S domains are structurally similar to the crotonase/isomerase superfamily, although only domain 1 of each 12S monomer binds ligand. The 12S reaction is similar to that of human propionyl-CoA carboxylase, whose beta-subunit has 50% sequence identity with 12S. A homology model of the propionyl-CoA carboxylase beta-subunit, based on this 12S crystal structure, provides new insight into the propionyl-CoA carboxylase mechanism, its oligomeric structure and the molecular basis of mutations responsible for enzyme deficiency in propionic acidemia.

Reviews - 1on3 mentioned but not cited (1)

  1. The enzymes of biotin dependent CO₂ metabolism: what structures reveal about their reaction mechanisms. Waldrop GL, Holden HM, St Maurice M. Protein Sci 21 1597-1619 (2012)

Articles - 1on3 mentioned but not cited (5)

  1. CASP5 target classification. Kinch LN, Qi Y, Hubbard TJ, Grishin NV. Proteins 53 Suppl 6 340-351 (2003)
  2. Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core. Hall PR, Wang YF, Rivera-Hainaj RE, Zheng X, Pustai-Carey M, Carey PR, Yee VC. EMBO J 22 2334-2347 (2003)
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  4. Crystallization and preliminary crystallographic analysis of DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase from Corynebacterium glutamicum. Yamada M, Natsume R, Nakamatsu T, Horinouchi S, Kawasaki H, Senda T. Acta Crystallogr Sect F Struct Biol Cryst Commun 63 120-122 (2007)
  5. Machine Learning-Supported Enzyme Engineering toward Improved CO2-Fixation of Glycolyl-CoA Carboxylase. Marchal DG, Schulz L, Schuster I, Ivanovska J, Paczia N, Prinz S, Zarzycki J, Erb TJ. ACS Synth Biol 12 3521-3530 (2023)


Reviews citing this publication (5)

  1. Structure and function of biotin-dependent carboxylases. Tong L. Cell Mol Life Sci 70 863-891 (2013)
  2. Fatty acid biosynthesis in actinomycetes. Gago G, Diacovich L, Arabolaza A, Tsai SC, Gramajo H. FEMS Microbiol Rev 35 475-497 (2011)
  3. Propionic acidemia: mutation update and functional and structural effects of the variant alleles. Desviat LR, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P, Clavero S, Ugarte M. Mol Genet Metab 83 28-37 (2004)
  4. Raman crystallography and other biochemical applications of Raman microscopy. Carey PR. Annu Rev Phys Chem 57 527-554 (2006)
  5. Functionally diverse biotin-dependent enzymes with oxaloacetate decarboxylase activity. Lietzan AD, St Maurice M. Arch Biochem Biophys 544 75-86 (2014)

Articles citing this publication (11)

  1. Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Lin TW, Melgar MM, Kurth D, Swamidass SJ, Purdon J, Tseng T, Gago G, Baldi P, Gramajo H, Tsai SC. Proc Natl Acad Sci U S A 103 3072-3077 (2006)
  2. Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase. Huang CS, Sadre-Bazzaz K, Shen Y, Deng B, Zhou ZH, Tong L. Nature 466 1001-1005 (2010)
  3. Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. Hall PR, Zheng R, Antony L, Pusztai-Carey M, Carey PR, Yee VC. EMBO J 23 3621-3631 (2004)
  4. Propionic acid fermentation by Propionibacterium freudenreichii CCTCC M207015 in a multi-point fibrous-bed bioreactor. Feng XH, Chen F, Xu H, Wu B, Yao J, Ying HJ, Ouyang PK. Bioprocess Biosyst Eng 33 1077-1085 (2010)
  5. Is dimerization required for the catalytic activity of bacterial biotin carboxylase? Shen Y, Chou CY, Chang GG, Tong L. Mol Cell 22 807-818 (2006)
  6. Proteins can convert to beta-sheet in single crystals. Zheng R, Zheng X, Dong J, Carey PR. Protein Sci 13 1288-1294 (2004)
  7. Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member. Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker C, Garcia-Diaz M, Tonge PJ. Biochemistry 50 9532-9544 (2011)
  8. Propionic acidemia as a cause of adult-onset dilated cardiomyopathy. Riemersma M, Hazebroek MR, Helderman-van den Enden ATJM, Salomons GS, Ferdinandusse S, Brouwers MCGJ, van der Ploeg L, Heymans S, Glatz JFC, van den Wijngaard A, Krapels IPC, Bierau J, Brunner HG. Eur J Hum Genet 25 1195-1201 (2017)
  9. Structural and biophysical characterization of BoxC from Burkholderia xenovorans LB400: a novel ring-cleaving enzyme in the crotonase superfamily. Bains J, Leon R, Boulanger MJ. J Biol Chem 284 16377-16385 (2009)
  10. Structural diversity in the six-fold redundant set of acyl-CoA carboxyltransferases in Mycobacterium tuberculosis. Holton SJ, King-Scott S, Nasser Eddine A, Kaufmann SH, Wilmanns M. FEBS Lett 580 6898-6902 (2006)
  11. Structural evidence for the involvement of the residues Ser187 and Tyr422 in substrate recognition in the 3-methylcrotonyl-coenzyme A carboxylase from Pseudomonas aeruginosa. Díaz-Pérez C, Díaz-Pérez AL, Rodríguez-Zavala JS, Campos-García J. J Biochem 154 291-297 (2013)


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