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PDBsum entry 1d0v
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The three-Dimensional structures of nicotinate mononucleotide:5,6- Dimethylbenzimidazole phosphoribosyltransferase (cobt) from salmonella typhimurium complexed with 5,6-Dimethybenzimidazole and its reaction products determined to 1.9 a resolution.
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Authors
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C.G.Cheong,
J.C.Escalante-Semerena,
I.Rayment.
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Ref.
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Biochemistry, 1999,
38,
16125-16135.
[DOI no: ]
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PubMed id
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Abstract
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Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase
(CobT) from Salmonella typhimurium plays a central role in the synthesis of
alpha-ribazole, which is a key component of the lower ligand of cobalamin. Two
X-ray structures of CobT are reported here at 1.9 A resolution. First, a complex
of CobT with 5,6-dimethylbenzimidazole, and second, a complex of CobT with its
reaction products, nicotinate and alpha-ribazole-5'-phosphate. CobT was
cocrystallized with 5,6-dimethylbenzimidazole (DMB) in the space group
P2(1)2(1)2 with unit cell dimensions of a = 72.1 A, b = 90.2 A, and c = 47.5 A
and one protomer per asymmetric unit. Subsequently, the crystals containing DMB
were soaked in nicotinate mononucleotide whereupon the physiological reaction
occurred in the crystal lattice to yield nicotinate and
alpha-ribazole-5'-phosphate. These studies show that CobT is a dimer where each
subunit consists of two domains. The large domain is dominated by a parallel
six-stranded beta-sheet with connecting alpha-helices that exhibit the topology
of a Rossmann fold. The small domain is made from components of the N- and
C-terminal sections of the polypeptide chain and contains a three-helix bundle.
The fold of CobT is unrelated to the type I and II phosphoribosylpyrophosphate
dependent transferases and does not appear to be related to any other protein
whose structure is known. The enzyme active site is located in a large cavity
formed by the loops at the C-terminal ends of the beta-strands and the small
domain of the neighboring subunit. DMB binds in a hydrophobic pocket created in
part by the neighboring small domain. This is consistent with the broad
specificity of this enzyme for aromatic substrates [Trzebiatowski, J. R.,
Escalante-Semerena (1997) J. Biol. Chem. 272, 17662-17667]. The binding site for
DMB suggests that Glu317 is the catalytic base required for the reaction. The
remainder of the cavity binds the nicotinate and ribose-5'-phosphate moieties,
which are nestled within the loops at the ends of the beta-strands.
Interestingly, the orientation of the substrate and products are opposite from
that expected for a Rossmann fold.
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