1ULZ

Crystal structure of the biotin carboxylase subunit of pyruvate carboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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:  
    1ULZ

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pyruvate carboxylase n-terminal domain451Aquifex aeolicus VF5Mutation(s): 1 
EC: 6.4.1.1
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
EPMRphasing
CNXrefinement
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