PDBsum entry: 2dzd

Ligase

PDB id: 2dzd

Contents

Protein chains

459 a.a. *

Waters ×349

* Residue conservation analysis

PDB id:

2dzd

Name:

Ligase

Title:

Crystal structure of the biotin carboxylase domain of pyruvate carboxylase

Structure:

Pyruvate carboxylase. Chain: a, b. Fragment: biotin carboxylase domain. Engineered: yes

Source:

Geobacillus thermodenitrificans. Organism_taxid: 33940. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.232 R-free: 0.290

Authors:

S.Kondo,Y.Nakajima,S.Sugio,S.Sueda,M.N.Islam,H.Kondo

Key ref:

S.Kondo et al. (2007). Structure of the biotin carboxylase domain of pyruvate carboxylase from Bacillus thermodenitrificans. Acta Crystallogr D Biol Crystallogr, 63, 885-890. PubMed id: 17642515 DOI: 10.1107/S0907444907029423

Date:

27-Sep-06 Release date: 25-Sep-07

Protein chains

Q05FZ3  (Q05FZ3_BACTC) -  Pyruvate carboxylase (Fragment)

Seq: 461 a.a.

Struc: 459 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (6 terms)

DOI no: 10.1107/S0907444907029423

Acta Crystallogr D Biol Crystallogr 63:885-890 (2007)

PubMed id: 17642515

Structure of the biotin carboxylase domain of pyruvate carboxylase from Bacillus thermodenitrificans.

S.Kondo, Y.Nakajima, S.Sugio, S.Sueda, M.N.Islam, H.Kondo.

ABSTRACT

The biotin carboxylase (BC) domain of pyruvate carboxylase (PC) from Bacillus thermodenitrificans (BC-bPC) was crystallized in an orthorhombic form (space group P2(1)2(1)2(1)), with unit-cell parameters a = 79.6, b = 116.0, c = 115.7 A. Two BC protomers are contained in the asymmetric unit. Diffraction data were collected at 100 K and the crystal structure was solved by the molecular-replacement method and refined against reflections in the 20.0-2.4 A resolution range, giving an R factor of 0.235 and a free R factor of 0.292. The overall structure of BC-bPC is similar to those of the BC subunits of Aquifex aeolicus PC (BC-aPC) and Escherichia coli ACC (BC-eACC). The crystal structure revealed that BC-bPC forms a unique dimeric quaternary structure, which might be caused as a result of the division of the BC domain from the rest of the protein. The position of domain B in BC-bPC differs from those in other enzymes of similar structure (BC-aPC and BC-eACC).

Selected figure(s)

Figure 1.
Figure 1 Overall schematic structure of BC-bPC illustrated using 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 6.
Figure 6 Three types of active-site structure of BC shown as stereoviews. (a), (b) and (c) show BC-bPC, unliganded BC-eACC (ATP-unbound open form) and liganded BC-eACC (ATP-bound closed form), respectively. The ATP models in (a) and (b) show the ATP model from liganded ACC virtually superimposed on the active site (light-coloured model).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 885-890) copyright 2007.

Figures were selected by an automated process.