Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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This is version 1.3 of the entry. See complete history


An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.

Deery, E.Schroeder, S.Lawrence, A.D.Taylor, S.L.Seyedarabi, A.Waterman, J.Wilson, K.S.Brown, D.Geeves, M.A.Howard, M.J.Pickersgill, R.W.Warren, M.J.

(2012) Nat Chem Biol 8: 933-940

  • DOI: https://doi.org/10.1038/nchembio.1086
  • Primary Citation of Related Structures:  
    3NJR, 4AU1, 4FDV

  • PubMed Abstract: 

    The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.

  • Organizational Affiliation

    School of Biosciences, University of Kent, Canterbury, Kent, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Precorrin-6y methylase
A, B
204Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: cobLRCAP_rcc02042
Find proteins for D5AV04 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AV04 
Go to UniProtKB:  D5AV04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AV04
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.354α = 90
b = 44.799β = 119.75
c = 84.11γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description