SirC, precorrin-2 dehydrogenase

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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This is version 1.2 of the entry. See complete history


Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase

Schubert, H.L.Rose, R.S.Leech, H.K.Brindley, A.A.Hill, C.P.Rigby, S.E.J.Warren, M.J.

(2008) Biochem J 415: 257-263

  • DOI: https://doi.org/10.1042/BJ20080785
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In Bacillus megaterium, the synthesis of vitamin B(12) (cobalamin) and sirohaem diverges at sirohydrochlorin along the branched modified tetrapyrrole biosynthetic pathway. This key intermediate is made by the action of SirC, a precorrin-2 dehydrogenase that requires NAD(+) as a cofactor. The structure of SirC has now been solved by X-ray crystallography to 2.8 A (1 A = 0.1 nm) resolution. The protein is shown to consist of three domains and has a similar topology to the multifunctional sirohaem synthases Met8p and the N-terminal region of CysG, both of which catalyse not only the dehydrogenation of precorrin-2 but also the ferrochelation of sirohydrochlorin to give sirohaem. Guided by the structure, in the present study a number of active-site residues within SirC were investigated by site-directed mutagenesis. No active-site general base was identified, although surprisingly some of the resulting protein variants were found to have significantly enhanced catalytic activity. Unexpectedly, SirC was found to bind metal ions such as cobalt and copper, and to bind them in an identical fashion with that observed in Met8p. It is suggested that SirC may have evolved from a Met8p-like protein by loss of its chelatase activity. It is proposed that the ability of SirC to act as a single monofunctional enzyme, in conjunction with an independent chelatase, may provide greater control over the intermediate at this branchpoint in the synthesis of sirohaem and cobalamin.

  • Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA. heidi@biochem.utah.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Precorrin-2 dehydrogenase
A, B
223Priestia megateriumMutation(s): 0 
Gene Names: sirC
Find proteins for P61818 (Priestia megaterium)
Explore P61818 
Go to UniProtKB:  P61818
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61818
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.595α = 90
b = 108.595β = 90
c = 201.028γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description