1CBF

THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase.

Schubert, H.L.Wilson, K.S.Raux, E.Woodcock, S.C.Warren, M.J.

(1998) Nat Struct Biol 5: 585-592

  • DOI: 10.1038/846
  • Primary Citation of Related Structures:  
    1CBF, 2CBF

  • PubMed Abstract: 
  • Biosynthesis of the corrin ring of vitamin B12 requires the action of six S-adenosyl-L-methionine (AdoMet) dependent transmethylases, closely related in sequence. The first X-ray structure of one of these, cobalt-precorrin-4 transmethylase, CbiF, from Bacillus megaterium has been determined to a resolution of 2 ...

    Biosynthesis of the corrin ring of vitamin B12 requires the action of six S-adenosyl-L-methionine (AdoMet) dependent transmethylases, closely related in sequence. The first X-ray structure of one of these, cobalt-precorrin-4 transmethylase, CbiF, from Bacillus megaterium has been determined to a resolution of 2.4 A. CbiF contains two alphabeta domains forming a trough in which S-adenosyl-L-homocysteine (AdoHcy) binds. The location of AdoHcy and a number of conserved residues, helps define the precorrin binding site. A second crystal form determined at 3.1 A resolution highlights the flexibility of two loops around this site. CbiF employs a unique mode of AdoHcy binding and represents a new class of transmethylase.


    Related Citations: 
    • Cobalamin (Vitamin B12) Biosynthesis--Cloning, Expression and Crystallisation of the Bacillus Megaterium S-Adenosyl-L-Methionine-Dependent Cobalt-Precorrin-4 Transmethylase Cbif
      Raux, E., Schubert, H.L., Woodcock, S.C., Wilson, K.S., Warren, M.J.
      (1998) Eur J Biochem 254: 341

    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COBALT-PRECORRIN-4 TRANSMETHYLASEA285Priestia megateriumMutation(s): 0 
Gene Names: cbiF
EC: 2.1.1.133 (PDB Primary Data), 2.1.1.271 (UniProt)
Find proteins for O87696 (Bacillus megaterium)
Explore O87696 
Go to UniProtKB:  O87696
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.7α = 90
b = 80.7β = 90
c = 109.4γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance