PDBsum entry 1jha

Go to PDB code: 
protein ligands links
Transferase PDB id
Protein chain
346 a.a. *
Waters ×133
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structural investigation of the biosynthesis of alternative ligands for cobamides by nicotinate mononucleotide:5,6- dimethylbenzimidazole phosphoribosyltransferase (cobt) from salmonella enterica
Structure: Nicotinate mononucleotide:5,6-dimethylbenzimidazo 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)
2.00Å     R-factor:   0.178     R-free:   0.275
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
27-Jun-01     Release date:   26-Sep-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q05603  (COBT_SALTY) -  Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
356 a.a.
346 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Corrin Biosynthesis (part 8)
      Reaction: Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate
Beta-nicotinate D-ribonucleotide
+ 5,6-dimethylbenzimidazole
Bound ligand (Het Group name = NIO)
corresponds exactly
alpha-ribazole 5'-phosphate
Bound ligand (Het Group name = AAM)
matches with 67.86% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     vitamin transmembrane transport   4 terms 
  Biochemical function     transferase activity     4 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19880598 K.R.Claas, J.R.Parrish, L.A.Maggio-Hall, and J.C.Escalante-Semerena (2010).
Functional analysis of the nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) enzyme, involved in the late steps of coenzyme B12 biosynthesis in Salmonella enterica.
  J Bacteriol, 192, 145-154.  
18083805 M.E.Taga, and G.C.Walker (2008).
Pseudo-B12 joins the cofactor family.
  J Bacteriol, 190, 1157-1159.  
17209023 C.L.Zayas, and J.C.Escalante-Semerena (2007).
Reassessment of the late steps of coenzyme B12 synthesis in Salmonella enterica: evidence that dephosphorylation of adenosylcobalamin-5'-phosphate by the CobC phosphatase is the last step of the pathway.
  J Bacteriol, 189, 2210-2218.  
17483216 J.C.Escalante-Semerena (2007).
Conversion of cobinamide into adenosylcobamide in bacteria and archaea.
  J Bacteriol, 189, 4555-4560.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.