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451 a.a.
Key reference
DOI no: 10.1107/S0907444904000423 Acta Crystallogr D Biol Crystallogr 60:486-492 (2004) PubMed id: 14993673
Structure of the biotin carboxylase subunit of pyruvate carboxylase from Aquifex aeolicus at 2.2 A resolution. S.Kondo, Y.Nakajima, S.Sugio, J.Yong-Biao, S.Sueda, H.Kondo. ABSTRACT
Pyruvate carboxylase (PC) is distributed in many eukaryotes as well as in some prokaryotes. PC catalyzes the ATP-dependent carboxylation of pyruvate to form oxalacetate. PC has three functional domains, one of which is a biotin carboxylase (BC) domain. The BC subunit of PC from Aquifex aeolicus (PC-beta) was crystallized in an orthorhombic form with space group P2(1)2(1)2, unit-cell parameters a = 92.4, b = 122.1, c = 59.0 A and one molecule in the asymmetric unit. Diffraction data were collected at 100 K on BL24XU at SPring-8. The crystal structure was determined by the molecular-replacement method and refined against 20.0-2.2 A resolution data, giving an R factor of 0.199 and a free R factor of 0.236. The crystal structure revealed that PC-beta forms a dimeric quaternary structure consisting of two molecules related by crystallographic twofold symmetry. The overall structure of PC-beta is similar to other biotin-dependent carboxylases, such as acetyl-CoA carboxylase (ACC). Although some parts of domain B were disordered in ACC, the corresponding parts of PC-beta were clearly determined in the crystal structure. From comparison between the active-site structure of ACC with ATP bound and a virtual model of PC-beta with ATP bound, it was shown that the backbone torsion angles of Glu203 in PC-beta change and some of water molecules in the active site of PC-beta are excluded upon ATP binding.
Selected figure(s)
Figure 1.
Figure 1 Overall schematic structure of PC-illustrated by the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]). Domains A, B and C are shown in red, green and blue, respectively.
Figure 2.
Figure 2 Topological diagram of PC--helices and loop regions are shown by arrows, rectangles and lines, respectively. The first and last residues are shown as numbers next to each secondary-structure element.
The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 486-492) copyright 2004. Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference
19213731 C.Y.Chou, L.P.Yu, and L.Tong (2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.J Biol Chem, 284, 11690-11697.
PDB codes: 3g8c 3g8d
17937401 O.Almog, A.Kogan, M.Leeuw, G.Y.Gdalevsky, R.Cohen-Luria, and A.H.Parola (2008).
Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41.Biopolymers, 89, 354-359.
18297087 S.Xiang, and L.Tong (2008).
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.Nat Struct Mol Biol, 15, 295-302.
PDB codes: 3bg3 3bg5 3bg9
17717183 M.St Maurice, L.Reinhardt, K.H.Surinya, P.V.Attwood, J.C.Wallace, W.W.Cleland, and I.Rayment (2007).
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.Science, 317, 1076-1079.
PDB code: 2qf7 The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.
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