PDBsum entry 1jhq

Transferase

PDB id: 1jhq

Contents

Protein chain

346 a.a. *

Ligands

PMO

NIO

Waters ×149

* Residue conservation analysis

PDB id:

1jhq

Name:

Transferase

Title:

Three-dimensional structure of cobt in complex with reaction products of 5-methoxybenzimidazole and namn

Structure:

Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase. Chain: a. Synonym: nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, nn:dbi prt. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.178 R-free: 0.279

Authors:

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

Key ref:

C.G.Cheong et al. (2001). Structural investigation of the biosynthesis of alternative lower ligands for cobamides by nicotinate mononucleotide: 5,6-dimethylbenzimidazole phosphoribosyltransferase from Salmonella enterica. J Biol Chem, 276, 37612-37620. PubMed id: 11441022 DOI: 10.1074/jbc.M105390200

Date:

28-Jun-01 Release date: 18-Oct-01

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 + nicotinate beta-D-ribonucleotide = alpha- ribazole 5'-phosphate (Bound ligand (Het Group name = PMO) matches with 84.62% similarity) + nicotinate + H(+) (Bound ligand (Het Group name = NIO) corresponds exactly)

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

reference

DOI no: 10.1074/jbc.M105390200

J Biol Chem 276:37612-37620 (2001)

PubMed id: 11441022

Structural investigation of the biosynthesis of alternative lower ligands for cobamides by nicotinate mononucleotide: 5,6-dimethylbenzimidazole phosphoribosyltransferase from Salmonella enterica.

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

ABSTRACT

Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole, a key component of the lower ligand of cobalamin. Surprisingly, CobT can phosphoribosylate a wide range of aromatic substrates, giving rise to a wide variety of lower ligands in cobamides. To understand the molecular basis for this lack of substrate specificity, the x-ray structures of CobT complexed with adenine, 5-methylbenzimidazole, 5-methoxybenzimidazole, p-cresol, and phenol were determined. Furthermore, adenine, 5-methylbenzimidazole, 5-methoxybenzimidazole, and 2-hydroxypurine were observed to react with NaMN within the crystal lattice and undergo the phosphoribosyl transfer reaction to form product. Significantly, the stereochemistries of all products are identical to those found in vivo. Interestingly, p-cresol and phenol, which are the lower ligand in Sporomusa ovata, bound to CobT but did not react with NaMN. This study provides a structural explanation for how CobT can phosphoribosylate most of the commonly observed lower ligands found in cobamides with the exception of the phenolic lower ligands observed in S. ovata. This is accomplished with minor conformational changes in the side chains that constitute the 5,6-dimethylbenzimidazole binding site. These investigations are consistent with the implication that the nature of the lower ligand is controlled by metabolic factors rather by the specificity of the phosphoribosyltransferase.

Selected figure(s)

Figure 4.
Fig. 4. Difference electron density for the ligands or products of the reaction with NaMN complexed with CobT. Shown are adenine (A), -adenosine monophosphate and nicotinate (B), 5-methylbenzimidazole (C), N1-(5-phospho- -ribosyl)-5-methylbenzimidazole and nicotinate (D), 5-methoxybenzimidazole (E), and N1-(5-phospho- -ribosyl)-5-methoxybenzimidazole and nicotinate (F). Coefficients of the form F[o] F[c] were utilized where the ligand was excluded from the phase calculation. The maps were contoured at the level of 1 .

Figure 6.
Fig. 6. Difference electron density for the reaction product for 2-hydroxypurine and NaMN , N1-(5-phospho- -ribosyl)-2-hydroxypurine, and nicotinate (A), p-cresol (B), p-cresol and nicotinate (C), phenol (D), and phenol and nicotinate complexed with CobT (E), respectively. Coefficients of the form F[o] F[c] were utilized, where the ligand was excluded from the phase calculation. The maps were contoured at the level of 1 .

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 37612-37620) copyright 2001.

Figures were selected by an automated process.