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PDBsum entry 1i9c
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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1i9c

 

 

 

 

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Contents
Protein chains
137 a.a. *
483 a.a. *
Ligands
B12 ×2
5AD ×2
GLU ×2
2AS ×2
Waters ×1258
* Residue conservation analysis
PDB id:
1i9c
Name: Isomerase
Title: Glutamate mutase from clostridium cochlearium: complex with adenosylcobalamin and substrate
Structure: Glutamate mutase. Chain: a, c. Synonym: methylaspartate mutase small chain. Engineered: yes. Glutamate mutase. Chain: b, d. Synonym: methylaspartate mutase e chain. Engineered: yes. Other_details: complexed with adenosylcobalamain and a mixture of
Source: Clostridium cochlearium. Organism_taxid: 1494. Atcc: dsm 1285. Collection: dsm 1285. Gene: glms. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: glme.
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.171     R-free:   0.221
Authors: K.Gruber,C.Kratky
Key ref: K.Gruber et al. (2001). Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase This work was supported by the Österreichische Akademie der Wissenschaften (APART fellowship 614), the Österreichische Fonds zur Förderung der wissenschaftlichen Forschung (FWF-project 11599), and the European Commission (TMR project number ERB 4061 PL 95-0307). Crystallographic data were collected at the EMBL-beamline BW7B at DESY in Hamburg, Germany. We thank the beamline scientists for their assistance, and Ingrid Dreveny, Günter Gartler, Gerwald Jogl, and Oliver Sauer for their help during data collection. This research emerged from a collaboration with Prof. W. Buckel (Marburg) who supplied us with clones of the glutamate mutase proteins. Angew Chem Int Ed Engl, 40, 3377-3380. PubMed id: 11592143
Date:
19-Mar-01     Release date:   19-Mar-02    
PROCHECK
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 Headers
 References

Protein chains
P80078  (GMSS_CLOCO) -  Glutamate mutase sigma subunit from Clostridium cochlearium
Seq:
Struc: 		137 a.a.
137 a.a.*
Protein chains
P80077  (GLME_CLOCO) -  Glutamate mutase epsilon subunit from Clostridium cochlearium
Seq:
Struc: 		483 a.a.
483 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.5.4.99.1  - methylaspartate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (2S,3S)-3-methyl-L-aspartate = L-glutamate
(2S,3S)-3-methyl-L-aspartate
 =
L-glutamate
Bound ligand (Het Group name = GLU)
corresponds exactly
      Cofactor: Cob(II)alamin
Cob(II)alamin
Bound ligand (Het Group name = B12) matches with 85.71% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Angew Chem Int Ed Engl 40:3377-3380 (2001)
PubMed id: 11592143  
 
 
Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase This work was supported by the Österreichische Akademie der Wissenschaften (APART fellowship 614), the Österreichische Fonds zur Förderung der wissenschaftlichen Forschung (FWF-project 11599), and the European Commission (TMR project number ERB 4061 PL 95-0307). Crystallographic data were collected at the EMBL-beamline BW7B at DESY in Hamburg, Germany. We thank the beamline scientists for their assistance, and Ingrid Dreveny, Günter Gartler, Gerwald Jogl, and Oliver Sauer for their help during data collection. This research emerged from a collaboration with Prof. W. Buckel (Marburg) who supplied us with clones of the glutamate mutase proteins.
K.Gruber, R.Reitzer, C.Kratky.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19630017 B.Durbeej, G.M.Sandala, D.Bucher, D.M.Smith, and L.Radom (2009).
On the importance of ribose orientation in the substrate activation of the coenzyme B12-dependent mutases.
  Chemistry, 15, 8578-8585.  
18586770 T.Toraya, N.Tamura, T.Watanabe, M.Yamanishi, N.Hieda, and K.Mori (2008).
Mechanism-based inactivation of coenzyme B12-dependent diol dehydratase by 3-unsaturated 1,2-diols and thioglycerol.
  J Biochem, 144, 437-446.  
16688781 L.Sun, and K.Warncke (2006).
Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features.
  Proteins, 64, 308-319.  
16156797 M.Fukuoka, Y.Nakanishi, R.B.Hannak, B.Kräutler, and T.Toraya (2005).
Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B12-dependent diol dehydratase and ethanolamine ammonia-lyase.
  FEBS J, 272, 4787-4796.  
15514022 F.Berkovitch, E.Behshad, K.H.Tang, E.A.Enns, P.A.Frey, and C.L.Drennan (2004).
A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.
  Proc Natl Acad Sci U S A, 101, 15870-15875.
PDB code: 1xrs
14527323 R.Banerjee, and S.W.Ragsdale (2003).
The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes.
  Annu Rev Biochem, 72, 209-247.  
12413543 K.Gruber, and C.Kratky (2002).
Coenzyme B(12) dependent glutamate mutase.
  Curr Opin Chem Biol, 6, 598-603.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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