1ID8

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

Summary for 1ID8

• Entry DOI: 10.2210/pdb1id8/pdb
• Related: 1CB7 1FMF
• Descriptor: METHYLASPARTATE MUTASE S CHAIN, 2-HYDROXY-PROPYL-AMMONIUM, PHOSPHORIC ACID MONO-[5-(5,6-DIMETHYL-BENZOIMIDAZOL-1-YL)-4-HYDROXY-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER (3 entities in total)
• Functional Keywords: coenzyme b12, ligand binding, nucleotide, protein nmr spectroscopy, protein folding, isomerase
• Biological source: Clostridium tetanomorphum
• Total number of polymer chains: 1
• Total formula weight: 15198.26

Authors

Tollinger, M.,Eichmuller, C.,Konrat, R.,Huhta, M.S.,Marsh, E.N.G.,Krautler, B. (deposition date: 2001-04-04, release date: 2001-06-27, Last modification date: 2024-05-22)

Primary citation

Tollinger, M.,Eichmuller, C.,Konrat, R.,Huhta, M.S.,Marsh, E.N.,Krautler, B.
The B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum traps the nucleotide moiety of coenzyme B(12).
J.Mol.Biol., 309:777-791, 2001

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. 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.

PubMed: 11397096
DOI: 10.1006/jmbi.2001.4696

Experimental method

SOLUTION NMR