Abstract
We gathered primary and tertiary structures of acyl-CoA carboxylases from public databases, and established that members of their biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains occur in one family each and that members of their carboxyl transferase (CT) domains occur in two families. Protein families have members similar in primary and tertiary structure that probably have descended from the same protein ancestor. The BCCP domains complexed with biotin in acyl and acyl-CoA carboxylases transfer bicarbonate ions from BC domains to CT domains, enabling the latter to carboxylate acyl and acyl-CoA moieties. We separated the BCCP domains into four subfamilies based on more subtle primary structure differences. Members of different BCCP subfamilies often are produced by different types of organisms and are associated with different carboxylases.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman, DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. http://blast.ncbi.nlm.nih.gov/Blast.cgi
Athappilly FK, Hendrickson WA (1995) Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. Structure 3:1407–1419
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2011) GenBank. Nucleic Acids Res 39:D32–D37. http://www.ncbi.nlm.nih.gov/protein
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242. http://www.pdb.org
Cantu DC, Chen Y, Reilly PJ (2010) Thioesterases: a new perspective based on their primary and tertiary structures. Protein Sci 19:1281–1295
Cantu DC, Chen Y, Lemons ML, Reilly PJ (2011) ThYme: a database for thioester-active enzymes. Nucleic Acids Res 39:D342–D346. http://enzyme.cbirc.iastate.edu
Cantu DC, Forrester MJ, Charov K, Reilly PJ (2012) Acyl carrier protein structural classification and normal mode analysis. Protein Sci 21:655–666
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282
Jordan IK, Henzeb K, Fedorova ND, Koonin EV, Galperin MY (2003) Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes. J Mol Microbiol Biotechnol 5:172–189
Lombard J, Moreira D (2011) Early evolution of the biotin-dependent carboxylase family. BMC Evol Biol 11:232
Mertz B, Kuczenski RS, Larsen RT, Hill AD, Reilly PJ (2005) Phylogenetic analysis of family 6 glycoside hydrolases. Biopolymers 79:197–206
NC-IUBMB (Nomenclature Committee of the International Union of Biochemistry and Molecular Biology). Enzyme nomenclature 1992. Academic Press, San Diego. http://www.chem.qmul.ac.uk/iubmb/enzyme/
Podkowiński J, Tworak A (2011) Acetyl-coenzyme A carboxylase—an attractive enzyme for biotechnology. BioTechnologia: J Biotechnol Computat Biol Bionanotechnol 92:321–335
Shatsky M, Nussinov R, Wolfson HJ (2004) A method for simultaneous alignment of multiple protein structures. Proteins 56:143–156. http://bioinfo3d.cs.tau.ac.il/MultiProt/
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Thelen JJ, Sergei S, Ohlrogge JB (2001) Brassicaceae express multiple isoforms of biotin carboxyl carrier protein in a tissue-specific manner. Plant Physiol 125:2016–2028
Toh H, Kondo H, Tanabe T (1993) Molecular evolution of biotin-dependent carboxylases. Eur J Biochem 215:687–696
UniProt Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38:D142–D148. http://www.uniprot.org/
Acknowledgments
This work was supported through National Science Foundation Grant EEC-0813570 to the Engineering Research Center for Biorenewable Chemicals, headquartered at Iowa State University and including Pennsylvania State University, Rice University, the University of California, Irvine, the University of New Mexico, the University of Virginia, and the University of Wisconsin-Madison. A. E.-N., an exchange student from the Tecnológico de Monterrey (México), participated in a National Science Foundation Research Experiences for Undergraduates program while being supported by Iowa State University. This article was written while the corresponding author was on a study leave at the School of Chemical Engineering, University of Queensland, Australia. He thanks his colleagues there for their hospitality. The authors thank Bryon Upton (Iowa State University) for his helpful comments.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Chen, Y., Elizondo-Noriega, A., Cantu, D.C. et al. Structural classification of biotin carboxyl carrier proteins. Biotechnol Lett 34, 1869–1875 (2012). https://doi.org/10.1007/s10529-012-0978-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10529-012-0978-4