1ID8

NMR STRUCTURE OF GLUTAMATE MUTASE (B12-BINDING SUBUNIT) COMPLEXED WITH THE VITAMIN B12 NUCLEOTIDE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum traps the nucleotide moiety of coenzyme B(12).

Tollinger, M.Eichmuller, C.Konrat, R.Huhta, M.S.Marsh, E.N.Krautler, B.

(2001) J Mol Biol 309: 777-791

  • DOI: 10.1006/jmbi.2001.4696
  • Primary Citation of Related Structures:  
    1ID8

  • PubMed Abstract: 
  • Glutamate mutase from Clostridium tetanomorphum binds coenzyme B(12) in a base-off/His-on form, in which the nitrogenous ligand of the B(12)-nucleotide function is displaced from cobalt by a conserved histidine. The effect of binding the B(12)-nucleotide moiety to MutS, the B(12)-binding subunit of glutamate mutase, was investigated using NMR spectroscopic methods ...

    Glutamate mutase from Clostridium tetanomorphum binds coenzyme B(12) in a base-off/His-on form, in which the nitrogenous ligand of the B(12)-nucleotide function is displaced from cobalt by a conserved histidine. The effect of binding the B(12)-nucleotide moiety to MutS, the B(12)-binding subunit of glutamate mutase, was investigated using NMR spectroscopic methods. Binding of the B(12)-nucleotide to MutS was determined to occur with K(d)=5.6(+/-0.7) mM and to be accompanied by a specific conformational change in the protein. The nucleotide binding cleft of the apo-protein, which is formed by a dynamic segment with propensity for partial alpha-helical conformation (the "nascent" alpha-helix), becomes completely structured upon binding of the B(12)-nucleotide, with formation of helix alpha1. In contrast, the segment containing the conserved residues of the B(12)-binding Asp-x-His-x-x-Gly motif remains highly dynamic in the protein/B(12)-nucleotide complex. From relaxation studies, the time constant tau, which characterizes the time scale for the formation of helix alpha1, was estimated to be about 30 micros (15)N and was the same in both, apo-protein and nucleotide-bound protein. Thus, the binding of the B(12)-nucleotide moiety does not significantly alter the kinetics of helix formation, but only shifts the equilibrium towards the structured fold. These results indicate MutS to be structured in such a way, as to be able to trap the nucleotide segment of the base-off form of coenzyme B(12) and provide, accordingly, the first structural clues as to how the process of B(12)-binding occurs.


    Related Citations: 
    • Adenosylcobalamin-dependent Glutamate Mutase from Clostridium Tetanomorphum. Overexpression in Escherichia coli, Purification, and Characterization of the Recombinant Enzyme
      Holloway, D.E., Marsh, E.N.
      (1994) J Biol Chem 269: 20425
    • How a Protein Prepares for B12 Binding: Structure and Dynamics of the B12-binding Subunit of Glutamate Mutase from Clostridium tetanomorphum
      Tollinger, M., Konrat, R., Hilbert, B.H., Marsh, E.N., Krautler, B.
      (1998) Structure 6: 1021

    Organizational Affiliation

    Institute of Organic Chemistry, University of Innsbruck, Innsbruck, A-6020, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLASPARTATE MUTASE S CHAINA137Clostridium tetanomorphumMutation(s): 0 
Gene Names: glmSmutS
EC: 5.4.99.1
UniProt
Find proteins for Q05488 (Clostridium tetanomorphum)
Explore Q05488 
Go to UniProtKB:  Q05488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05488
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DBI
Query on DBI

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHORIC ACID MONO-[5-(5,6-DIMETHYL-BENZOIMIDAZOL-1-YL)-4-HYDROXY-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER
C14 H19 N2 O7 P
JIABVZWSYKDHDJ-SYQHCUMBSA-N
 Ligand Interaction
FOP
Query on FOP

Download Ideal Coordinates CCD File 
B [auth A]2-HYDROXY-PROPYL-AMMONIUM
C3 H10 N O
HXKKHQJGJAFBHI-GSVOUGTGSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 1ID8 Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Database references, Derived calculations