1L4F

The crystal structure of CobT complexed with 4,5-dimethyl-1,2-phenylenediamine and nicotinate mononucleotide

Summary for 1L4F

• Entry DOI: 10.2210/pdb1l4f/pdb
• Related: 1D0S 1L4B 1L4E 1L4G 1L4H 1L4K 1L4L 1L4M 1L4N 1L5F 1L5K 1L5L 1L5M 1L5N 1L5O
• Descriptor: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, 4,5-DIMETHYL-1,2-PHENYLENEDIAMINE, NICOTINATE MONONUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: cobt, cobalamin synthetic enzyme, phosphoribosyltransferase, 5, 6-dimethylbenzimidazole, nicotinate mononucleotide, transferase
• Biological source: Salmonella enterica
• Total number of polymer chains: 1
• Total formula weight: 37146.99

Authors

Cheong, C.-G.,Escalante-Semerena, J.,Rayment, I. (deposition date: 2002-03-06, release date: 2002-09-07, Last modification date: 2024-11-20)

Primary citation

Cheong, C.G.,Escalante-Semerena, J.C.,Rayment, I.
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., 277:41120-41127, 2002

PubMed Abstract: Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin. In earlier studies it proved difficult to obtain the structure of CobT bound to NaMN because it is hydrolyzed in the crystal lattice in the absence of the second substrate DMB. In an effort to map the reaction pathway of this enzyme, NaMN was captured in the active site with the substrate analogs 4,5-dimethyl-1,2-phenylenediamine, 4-methylcatechol, indole, 3,4-dimethylaniline, 2,5-dimethylaniline, 3,4-dimethylphenol, and 2-amino-p-cresol. Structures of these complexes reveal that they exclude water molecules responsible for the hydrolysis from the active site. These structures, together with the early complexes with alpha-ribazole-5'-phosphate and DMB, provide a complete description of the reaction pathway. They demonstrate that the nicotinate moiety and phosphate do not appear to move significantly between reactants and products but that the aromatic base and ribose moiety each move approximately 1.2 A toward each other in the transformation. This study also reveals that, like many other nucleotide binding proteins, coordination of DMB is accompanied by a disorder-order transition in a surface loop. The structure of apo-CobT is also reported.

PubMed: 12101181
DOI: 10.1074/jbc.M203535200

Experimental method

X-RAY DIFFRACTION (2.1 Å)