Crystal structure of the biotin carboxylase subunit of pyruvate carboxylase

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Structure of the biotin carboxylase subunit of pyruvate carboxylase from Aquifex aeolicus at 2.2 A resolution.

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

(2004) Acta Crystallogr D Biol Crystallogr 60: 486-492

  • DOI: https://doi.org/10.1107/S0907444904000423
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    MCC Group Science and Technology Research Center, Mitsubishi Chemical Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pyruvate carboxylase n-terminal domain451Aquifex aeolicus VF5Mutation(s): 1 
Find proteins for O67483 (Aquifex aeolicus (strain VF5))
Explore O67483 
Go to UniProtKB:  O67483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67483
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.418α = 90
b = 122.145β = 90
c = 59.011γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-12-27
    Changes: Data collection