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PDBsum entry 1d0s

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protein ligands links
Transferase PDB id
1d0s
Jmol
Contents
Protein chain
346 a.a. *
Ligands
PO4
DMD
Waters ×132
* Residue conservation analysis
PDB id:
1d0s
Name: Transferase
Title: Crystal structure of nicotinate mononucleotide : 5,6- dimethylbenzimidazole phosphoribosyltransferase (cobt) from salmonella typhimurium complexed with 5, 6-dimethylbenzimid
Structure: Nicotinate mononucleotide:5,6-dimethylbenzimidazo phosphoribosyltransferase. Chain: a. Ec: 2.4.2.21
Source: Salmonella typhimurium. Organism_taxid: 602
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.172    
Authors: C.-G.Cheong,J.C.Escalante-Semerena,I.Rayment
Key ref:
C.G.Cheong et al. (1999). 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, 38, 16125-16135. PubMed id: 10587435 DOI: 10.1021/bi991752c
Date:
14-Sep-99     Release date:   29-Dec-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q05603  (COBT_SALTY) -  Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Seq:
Struc:
356 a.a.
346 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.21  - Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
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 = DMD)
corresponds exactly
= nicotinate
+ alpha-ribazole 5'-phosphate
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  

 

 
    reference    
 
 
DOI no: 10.1021/bi991752c Biochemistry 38:16125-16135 (1999)
PubMed id: 10587435  
 
 
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.
C.G.Cheong, J.C.Escalante-Semerena, I.Rayment.
 
  ABSTRACT  
 
Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella typhimurium plays a central role in the synthesis of alpha-ribazole, which is a key component of the lower ligand of cobalamin. Two X-ray structures of CobT are reported here at 1.9 A resolution. First, a complex of CobT with 5,6-dimethylbenzimidazole, and second, a complex of CobT with its reaction products, nicotinate and alpha-ribazole-5'-phosphate. CobT was cocrystallized with 5,6-dimethylbenzimidazole (DMB) in the space group P2(1)2(1)2 with unit cell dimensions of a = 72.1 A, b = 90.2 A, and c = 47.5 A and one protomer per asymmetric unit. Subsequently, the crystals containing DMB were soaked in nicotinate mononucleotide whereupon the physiological reaction occurred in the crystal lattice to yield nicotinate and alpha-ribazole-5'-phosphate. These studies show that CobT is a dimer where each subunit consists of two domains. The large domain is dominated by a parallel six-stranded beta-sheet with connecting alpha-helices that exhibit the topology of a Rossmann fold. The small domain is made from components of the N- and C-terminal sections of the polypeptide chain and contains a three-helix bundle. The fold of CobT is unrelated to the type I and II phosphoribosylpyrophosphate dependent transferases and does not appear to be related to any other protein whose structure is known. The enzyme active site is located in a large cavity formed by the loops at the C-terminal ends of the beta-strands and the small domain of the neighboring subunit. DMB binds in a hydrophobic pocket created in part by the neighboring small domain. This is consistent with the broad specificity of this enzyme for aromatic substrates [Trzebiatowski, J. R., Escalante-Semerena (1997) J. Biol. Chem. 272, 17662-17667]. The binding site for DMB suggests that Glu317 is the catalytic base required for the reaction. The remainder of the cavity binds the nicotinate and ribose-5'-phosphate moieties, which are nestled within the loops at the ends of the beta-strands. Interestingly, the orientation of the substrate and products are opposite from that expected for a Rossmann fold.
 

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.  
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.  
12101181 C.G.Cheong, J.C.Escalante-Semerena, and I.Rayment (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.  
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