1D0V

CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.160 

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This is version 1.4 of the entry. See complete history


Literature

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.

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

(1999) Biochemistry 38: 16125-16135

  • DOI: 10.1021/bi991752c
  • Primary Citation of Related Structures:  
    1D0S, 1D0V

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Institute for Enzyme Research, Department of Biochemistry, University of Wisconsin, Madison 53705, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASEA356Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 2.4.2.21
UniProt
Find proteins for Q05603 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q05603 
Go to UniProtKB:  Q05603
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBZ (Subject of Investigation/LOI)
Query on RBZ

Download Ideal Coordinates CCD File 
B [auth A]ALPHA-RIBAZOLE-5'-PHOSPHATE
C14 H19 N2 O7 P
ZMRGXEJKZPRBPJ-SYQHCUMBSA-N
 Ligand Interaction
NIO
Query on NIO

Download Ideal Coordinates CCD File 
C [auth A]NICOTINIC ACID
C6 H5 N O2
PVNIIMVLHYAWGP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.1α = 90
b = 90β = 90
c = 47.6γ = 90
Software Package:
Software NamePurpose
FRAMBOdata collection
XDSdata reduction
SOLVEphasing
TNTrefinement
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation