PDBsum entry: 1ulz

Ligase

PDB id: 1ulz

Contents

Protein chain

451 a.a. *

Waters ×275

* Residue conservation analysis

PDB id:

1ulz

Name:

Ligase

Title:

Crystal structure of the biotin carboxylase subunit of pyruv carboxylase

Structure:

Pyruvate carboxylase n-terminal domain. Chain: a. Fragment: residues 1-451. Synonym: biotin carboxylase, subunit of pyruvate carboxylas engineered: yes. Mutation: yes

Source:

Aquifex aeolicus. Organism_taxid: 224324. Strain: vf5. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.201 R-free: 0.236

Authors:

S.Kondo,Y.Nakajima,S.Sugio,J.Yong-Biao,S.Sueda,H.Kondo

Key ref:

S.Kondo et al. (2004). Structure of the biotin carboxylase subunit of pyruvate carboxylase from Aquifex aeolicus at 2.2 A resolution. Acta Crystallogr D Biol Crystallogr, 60, 486-492. PubMed id: 14993673 DOI: 10.1107/S0907444904000423

Date:

18-Sep-03 Release date: 09-Mar-04

Protein chain

O67483  (O67483_AQUAE) -  Pyruvate carboxylase n-terminal domain

Seq: 472 a.a.

Struc: 451 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

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

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- . Domains A, B and C are shown in red, green and blue, respectively. The -strands, -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.