1CCW

STRUCTURE OF THE COENZYME B12 DEPENDENT ENZYME GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights

Reitzer, R., Gruber, K., Jogl, G., Wagner, U.G., Bothe, H., Buckel, W., Kratky, C.

(1999) Structure 7: 891-902

  • DOI: https://doi.org/10.1016/s0969-2126(99)80116-6
  • Primary Citation of Related Structures:  
    1CB7, 1CCW

  • PubMed Abstract: 

    • Glutamate mutase (Glm) equilibrates (S)-glutamate with (2S,3S)-3-methylaspartate. Catalysis proceeds with the homolytic cleavage of the organometallic bond of the cofactor to yield a 5'-desoxyadenosyl radical. This radical then abstracts a hydrogen atom from the protein-bound substrate to initiate the rearrangement reaction ...

    Glutamate mutase (Glm) equilibrates (S)-glutamate with (2S,3S)-3-methylaspartate. Catalysis proceeds with the homolytic cleavage of the organometallic bond of the cofactor to yield a 5'-desoxyadenosyl radical. This radical then abstracts a hydrogen atom from the protein-bound substrate to initiate the rearrangement reaction. Glm from Clostridium cochlearium is a heterotetrameric molecule consisting of two sigma and two epsilon polypeptide chains.

    Related Citations: 
    • Crystallization and preliminary X-ray analysis of recombinant glutamate mutase and of the isolated component S from Clostridium cochlearium.
      Reitzer, R., Krasser, M., Jogl, G., Buckel, W., Bothe, H., Kratky, C.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1039
    • Characterization of the coenzyme-B12-dependent glutamate mutase from Clostridium cochlearium produced in Escherichia coli.
      Zelder, O., Beatrix, B., Leutbecher, U., Buckel, W.
      (1994) Eur J Biochem 226: 577
    Organizational Affiliation: 

    Abteilung für Strukturbiologie, Institut für Physikalische Chemie, Karl-Franzens-Universität, Graz, Austria.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GLUTAMATE MUTASE)
A, C
137Clostridium cochleariumMutation(s): 0 
Gene Names: glmS
EC: 5.4.99.1
UniProt
Find proteins for P80078 (Clostridium cochlearium)
Explore P80078 
Go to UniProtKB:  P80078
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80078
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GLUTAMATE MUTASE)
B, D
483Clostridium cochleariumMutation(s): 0 
Gene Names: glmE
EC: 5.4.99.1
UniProt
Find proteins for P80077 (Clostridium cochlearium)
Explore P80077 
Go to UniProtKB:  P80077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80077
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNC
Query on CNC
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		CYANOCOBALAMIN
C63 H89 Co N14 O14 P
SYZBZQWSWIJYAR-UVKKECPRSA-M		 Ligand Interaction
TAR
Query on TAR
Download Ideal Coordinates CCD File 
F [auth B],
H [auth D]		D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TAR Binding MOAD:  1CCW Ki: 1.00e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Observed: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.43α = 90
b = 113.05β = 95.79
c = 108.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CCP4model building
SHELXL-97refinement
CCP4data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-01
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references
  • Version 2.0: 2021-08-18
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary