PDBsum entry 1be1

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Isomerase PDB id
Protein chain
137 a.a. *
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Glutamate mutase (b12-binding subunit), nmr, minimized average structure
Structure: Glutamate mutase. Chain: a. Fragment: b12-binding subunit. Synonym: muts. Engineered: yes
Source: Clostridium tetanomorphum. Organism_taxid: 1553. Strain: h1. Atcc: atcc 15920. Collection: atcc 15920. Gene: muts. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: M.Tollinger,R.Konrat,B.H.Hilbert,E.N.G.Marsh,B.Kraeutler
Key ref:
M.Tollinger et al. (1998). How a protein prepares for B12 binding: structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium tetanomorphum. Structure, 6, 1021-1033. PubMed id: 9739092 DOI: 10.1016/S0969-2126(98)00103-8
19-May-98     Release date:   26-Aug-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q05488  (MAMA_CLOTT) -  Glutamate mutase sigma subunit
137 a.a.
137 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Methylaspartate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-threo-3-methylaspartate = L-glutamate
= L-glutamate
      Cofactor: Cob(I)alamin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     anaerobic glutamate catabolic process   2 terms 
  Biochemical function     isomerase activity     5 terms  


DOI no: 10.1016/S0969-2126(98)00103-8 Structure 6:1021-1033 (1998)
PubMed id: 9739092  
How a protein prepares for B12 binding: structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium tetanomorphum.
M.Tollinger, R.Konrat, B.H.Hilbert, E.N.Marsh, B.Kräutler.
BACKGROUND: Glutamate mutase is an adenosylcobamide (coenzyme B12) dependent enzyme that catalyzes the reversible rearrangement of (2S)-glutamate to (2S,3S)-3-methylaspartate. The enzyme from Clostridium tetanomorphum comprises two subunits (of 53.7 and 14.8 kDa) and in its active form appears to be an alpha 2 beta 2 tetramer. The smaller subunit, termed MutS, has been characterized as the B12-binding component. Knowledge on the structure of a B12-binding apoenzyme does not exist. RESULTS: The solution structure and important dynamical aspects of MutS have been determined from a heteronuclear NMR study. The global fold of MutS in solution resembles that determined by X-ray crystallography for the B12-binding domains of Escherichia coli methionine synthase and Propionibacterium shermanii methylmalonyl CoA mutase. In these two proteins a histidine residue displaces the endogenous cobalt-coordinating ligand of the B12 cofactor. In MutS, however, the segment of the protein containing the conserved histidine residue forms part of an unstructured and mobile extended loop. CONCLUSIONS: A comparison of the crystal structures of two B12-binding domains, with bound B12 cofactor, and the solution structure of the apoprotein MutS has helped to clarify the mechanism of B12 binding. The major part of MutS is preorganized for B12 binding, but the B12-binding site itself is only partially formed. Upon binding B12, important elements of the binding site appear to become structured, including an alpha helix that forms one side of the cleft accommodating the nucleotide 'tail' of the cofactor.
  Selected figure(s)  
Figure 1.
Figure 1. The chemical structures of B[12] derivatives. The general formula is given on the left, variation of the organic ligand R and/or of the nucleotide base gives rise to the different organometallic cobamides: coenzyme B[12] (1), 5'-deoxy-5'-adenosyl-adeninylcobamide (pseudo-coenzyme B[12]; 1b) and methylcobalamin (2).
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1021-1033) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17419733 C.D.Richter, D.A.Stanmore, R.N.Miguel, M.C.Moncrieffe, L.Tran, S.Brewerton, F.Meersman, R.W.Broadhurst, and K.J.Weissman (2007).
Autonomous folding of interdomain regions of a modular polyketide synthase.
  FEBS J, 274, 2196-2209.  
12413543 K.Gruber, and C.Kratky (2002).
Coenzyme B(12) dependent glutamate mutase.
  Curr Opin Chem Biol, 6, 598-603.  
11893736 M.Vlasie, S.Chowdhury, and R.Banerjee (2002).
Importance of the histidine ligand to coenzyme B12 in the reaction catalyzed by methylmalonyl-CoA mutase.
  J Biol Chem, 277, 18523-18527.  
11738186 P.M.Kozlowski (2001).
Quantum chemical modeling of Co--C bond activation in B(12)-dependent enzymes.
  Curr Opin Chem Biol, 5, 736-743.  
11571143 P.Robinson, K.Neelon, H.J.Schreier, and M.F.Roberts (2001).
beta-Glutamate as a substrate for glutamine synthetase.
  Appl Environ Microbiol, 67, 4458-4463.  
11371179 R.Banerjee (2001).
Radical peregrinations catalyzed by coenzyme B12-dependent enzymes.
  Biochemistry, 40, 6191-6198.  
10940017 B.Hoffmann, M.Oberhuber, E.Stupperich, H.Bothe, W.Buckel, R.Konrat, and B.Kräutler (2000).
Native corrinoids from Clostridium cochlearium are adeninylcobamides: spectroscopic analysis and identification of pseudovitamin B(12) and factor A.
  J Bacteriol, 182, 4773-4782.  
10956023 I.Roymoulik, N.Moon, W.R.Dunham, D.P.Ballou, and E.N.Marsh (2000).
Rearrangement of L-2-hydroxyglutarate to L-threo-3-methylmalate catalyzed by adenosylcobalamin-dependent glutamate mutase.
  Biochemistry, 39, 10340-10346.  
10531377 A.Ratnatilleke, J.W.Vrijbloed, and J.A.Robinson (1999).
Cloning and sequencing of the coenzyme B(12)-binding domain of isobutyryl-CoA mutase from Streptomyces cinnamonensis, reconstitution of mutase activity, and characterization of the recombinant enzyme produced in Escherichia coli.
  J Biol Chem, 274, 31679-31685.  
10429202 B.Hoffmann, R.Konrat, H.Bothe, W.Buckel, and B.Kräutler (1999).
Structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium cochlearium.
  Eur J Biochem, 263, 178-188.
PDB code: 1b1a
10215883 K.Sauer, and R.K.Thauer (1999).
Methanol:coenzyme M methyltransferase from Methanosarcina barkeri -- substitution of the corrinoid harbouring subunit MtaC by free cob(I)alamin.
  Eur J Biochem, 261, 674-681.  
10467140 N.Shibata, J.Masuda, T.Tobimatsu, T.Toraya, K.Suto, Y.Morimoto, and N.Yasuoka (1999).
A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
  Structure, 7, 997.
PDB code: 1dio
10467146 R.Reitzer, K.Gruber, G.Jogl, U.G.Wagner, H.Bothe, W.Buckel, and C.Kratky (1999).
Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.
  Structure, 7, 891-902.
PDB codes: 1cb7 1ccw
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.