PDBsum entry 1l4h

Transferase

PDB id: 1l4h

Contents

Protein chain

346 a.a. *

Ligands

IND

NCN

Waters ×97

* Residue conservation analysis

PDB id:

1l4h

Name:

Transferase

Title:

Crystal structure of cobt complexed with indole and nicotinate mononucleotide

Structure:

Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase. Chain: a. Synonym: cobt. Nn:dbi prt. N1-alpha-phosphoribosyltransferase. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase. Engineered: yes

Source:

Salmonella enterica. Organism_taxid: 28901. Gene: cobt. Expressed in: salmonella enterica. Expression_system_taxid: 28901.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.10Å R-factor: 0.175 R-free: 0.209

Authors:

C.-G.Cheong,J.Escalante-Semerena,I.Rayment

Key ref:

C.G.Cheong et al. (2002). 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. PubMed id: 12101181

Date:

06-Mar-02 Release date: 07-Sep-02

Protein chain

Q05603  (COBT_SALTY) -  Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 356 a.a.

Struc: 346 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.4.2.21 - nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase.
• Pathway: Corrin Biosynthesis (part 8)
• Reaction: 5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha- ribazole 5'-phosphate + nicotinate + H⁺

5,6-dimethylbenzimidazole (Bound ligand (Het Group name = IND) matches with 81.82% similarity) + nicotinate beta-D-ribonucleotide = alpha- ribazole 5'-phosphate (Bound ligand (Het Group name = NCN) matches with 76.92% similarity) + nicotinate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Biol Chem 277:41120-41127 (2002)

PubMed id: 12101181

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.

C.G.Cheong, J.C.Escalante-Semerena, I.Rayment.

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.