PDBsum entry 1l5o

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Transferase PDB id
Protein chain
346 a.a. *
Waters ×178
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of cobt complexed with 3,4-dimethylphenol nicotinate mononucleotide
Structure: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase. Chain: a. Synonym: cobt. Nn:dbi prt. N1-alpha-phosphoribosyltransfera 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)
1.60Å     R-factor:   0.174     R-free:   0.199
Authors: C.-G.Cheong,J.Escalante-Semerena,I.Rayment
Key ref:
C.G.Cheong et al. (2002). Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes. Biochemistry, 41, 9079-9089. PubMed id: 12119022 DOI: 10.1021/bi020294w
07-Mar-02     Release date:   07-Sep-02    
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
Bound ligand (Het Group name = NCN)
corresponds exactly
Bound ligand (Het Group name = 2MP)
matches with 66.67% similarity
= 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  


DOI no: 10.1021/bi020294w Biochemistry 41:9079-9089 (2002)
PubMed id: 12119022  
Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
C.G.Cheong, J.C.Escalante-Semerena, I.Rayment.
The evolution of biosynthetic pathways is difficult to reconstruct in hindsight; however, the structures of the enzymes that are involved may provide insight into their development. One enzyme in the cobalamin biosynthetic pathway that appears to have evolved from a protein with different function is L-threonine-O-3-phosphate decarboxylase (CobD) from Salmonella enterica, which is structurally similar to histidinol phosphate aminotransferase [Cheong, C. G., Bauer, C. B., Brushaber, K. R., Escalante-Semerena, J. C., and Rayment, I. (2002) Biochemistry 41, 4798-4808]. This enzyme is responsible for synthesizing (R)-1-amino-2-propanol phosphate which is the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin. To understand the relationship between this decarboxylase and the aspartate aminotransferase family to which it belongs, the structures of CobD in its apo state, the apo state complexed with the substrate, and its product external aldimine complex have been determined at 1.46, 1.8, and 1.8 A resolution, respectively. These structures show that the enzyme steers the breakdown of the external aldimine toward decarboxylation instead of amino transfer by positioning the carboxylate moiety of the substrate out of the plane of the pyridoxal ring and by placing the alpha-hydrogen out of reach of the catalytic base provided by the lysine that forms the internal aldimine. It would appear that CobD evolved from a primordial PLP-dependent aminotransferase, where the selection was based on similarities between the stereochemical properties of the substrates rather than preservation of the fate of the external aldimine. These structures provide a sequence signature for distinguishing between L-threonine-O-3-phosphate decarboxylase and histidinol phosphate aminotransferases, many of which appear to have been misannotated.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18560156 J.Marienhagen, T.Sandalova, H.Sahm, L.Eggeling, and G.Schneider (2008).
Insights into the structural basis of substrate recognition by histidinol-phosphate aminotransferase from Corynebacterium glutamicum.
  Acta Crystallogr D Biol Crystallogr, 64, 675-685.
PDB codes: 3cq4 3cq5 3cq6
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