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EC Number

Catalytic Site Atlas

CSA LITERATURE entry for 1d0s

E.C. namenicotinate-nucleotide---dimethylbenzimidazole phosphoribosyltransferase
SpeciesSalmonella typhimurium (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1d0sThere are 29 Homologs
CSA Entries With UniProtID Q05603
CSA Entries With EC Number
PDBe Entry 1d0s
PDBSum Entry 1d0s
MACiE Entry M0079

Literature Report

IntroductionNicotinate mononucleotide:5,6- dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) is crucial in the synthesis of alpha-ribose-5'-phosphate, a precursor to the lower ligand of colbamin. The biosynthesis of colbamin requires more than 25 committed enzymes, and the biosynthetic pathway has received much interest because of its complexity. Colbamin synthesis is also of interest in evolutionary biology because of its utilisation by early forms of bacteria and Archaea.
MechansimThe carboxylate side chain of Glu317 acts as a catalytic base, abstracting the proton of the N3 of DMB, whereupon the N1 atom attacks the C1' carbon of ribose with concerted displacement of the nicotinate ring. This leads to the direct displacement reaction, with a inversion of configuration of the carbon centre.

Catalytic Sites for 1d0s

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA317317macie:sideChainThe residue acts as a general base towards the DMB substrate, deprotonating the N3 position. This leads to conjugate attack through the N1 atom at the nictotinate D-ribonucleotide substrate in a concerted SN2 displacement reaction, resulting in an inversion of configuration at the carbon centre.

Literature References

Cheong CG
Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica.
J Biol Chem 2002 277 41120-41127
PubMed: 12101181
Cheong CG
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.
Biochemistry 1999 38 16125-16135
PubMed: 10587435