1BMT

HOW A PROTEIN BINDS B12: A 3.O ANGSTROM X-RAY STRUCTURE OF THE B12-BINDING DOMAINS OF METHIONINE SYNTHASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase.

Drennan, C.L., Huang, S., Drummond, J.T., Matthews, R.G., Ludwig, M.L.

(1994) Science 266: 1669-1674

  • DOI: 10.1126/science.7992050
  • Primary Citation of Related Structures:  
    1BMT

  • PubMed Abstract: 

    • The crystal structure of a 27-kilodalton methylcobalamin-containing fragment of methionine synthase from Escherichia coli was determined at 3.0 A resolution. This structure depicts cobalamin-protein interactions and reveals that the corrin macrocycle lies between a helical amino-terminal domain and an alpha/beta carboxyl-terminal domain that is a variant of the Rossmann fold ...

    The crystal structure of a 27-kilodalton methylcobalamin-containing fragment of methionine synthase from Escherichia coli was determined at 3.0 A resolution. This structure depicts cobalamin-protein interactions and reveals that the corrin macrocycle lies between a helical amino-terminal domain and an alpha/beta carboxyl-terminal domain that is a variant of the Rossmann fold. Methylcobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in the adenosylcobalamin-dependent enzymes methylmalonyl-coenzyme A mutase and glutamate mutase, suggesting that displacement of the dimethylbenzimidazole will be a feature common to many cobalamin-binding proteins. Thus the cobalt ligand, His759, and the neighboring residues Asp757 and Ser810, may form a catalytic quartet, Co-His-Asp-Ser, that modulates the reactivity of the B12 prosthetic group in methionine synthase.

    Related Citations: 
    • Cobalamin-Dependent Methionine Synthase: The Structure of a Methylcobalamin-Binding Fragment and Implications for Other B12-Dependent Enzymes
      Drennan, C.L., Matthews, R.G., Ludwig, M.L.
      (1994) Curr Opin Struct Biol 4: 919
    Organizational Affiliation: 

    Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHIONINE SYNTHASEA, B246Escherichia coliMutation(s): 0 
EC: 2.1.1.13
UniProt
Find proteins for P13009 (Escherichia coli (strain K12))
Explore P13009 
Go to UniProtKB:  P13009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13009
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COB
Query on COB
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		CO-METHYLCOBALAMIN
C63 H91 Co N13 O14 P
BMOGZGJBQIUQJG-BYLSPCLQSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.7α = 90
b = 55.3β = 90
c = 103.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-04-27
    Changes: Database references, Derived calculations, Other, Source and taxonomy