2DJ5

Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the Vitamin B(12) Biosynthetic Cobaltochelatase, CbiX (S), from Archaeoglobus Fulgidus

Yin, J.Xu, L.X.Cherney, M.M.Raux-Deery, E.Bindley, A.A.Savchenko, A.Walker, J.R.Cuff, M.E.Warren, M.J.James, M.N.G.

(2006) J Struct Funct Genomics 7: 37-50

  • DOI: https://doi.org/10.1007/s10969-006-9008-x
  • Primary Citation of Related Structures:  
    2DJ5

  • PubMed Abstract: 

    The Archaeoglobus fulgidus gene af0721 encodes CbiX(S), a small cobaltochelatase associated with the anaerobic biosynthesis of vitamin B12 (cobalamin). The protein was shown to have activity both in vivo and in vitro, catalyzing the insertion of Co2+ into sirohydrochlorin. The structure of CbiX(S) was determined in two different crystal forms and was shown to consist of a central mixed beta-sheet flanked by four alpha-helices, one of which originates in the C-terminus of a neighboring molecule. CbiX(S) is about half the size of other Class II tetrapyrrole chelatases. The overall topography of CbiX(S) exhibits substantial resemblance to both the N- and C-terminal regions of several members of the Class II metal chelatases involved in tetrapyrrole biosynthesis. Two histidines (His10 and His74), are in similar positions as the catalytic histidine residues in the anaerobic cobaltochelatase CbiK (His145 and His207). In light of the hypothesis that suggests the larger chelatases evolved via gene duplication and fusion from a CbiX(S)-like enzyme, the structure of AF0721 may represent that of an "ancestral" precursor of class II metal chelatases.


  • Organizational Affiliation

    Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada, T6G 2H7.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sirohydrochlorin cobaltochelatase
A, B
133Archaeoglobus fulgidusMutation(s): 0 
Gene Names: cbiX
EC: 4.99.1.3
UniProt
Find proteins for O29537 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29537 
Go to UniProtKB:  O29537
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29537
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.721α = 90
b = 62.721β = 90
c = 150.609γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description