4KQK

Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Dissecting cobamide diversity through structural and functional analyses of the base-activating CobT enzyme of Salmonella enterica.

Chan, C.H.Newmister, S.A.Talyor, K.Claas, K.R.Rayment, I.Escalante-Semerena, J.C.

(2014) Biochim.Biophys.Acta 1840: 464-475

  • DOI: 10.1016/j.bbagen.2013.09.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cobamide diversity arises from the nature of the nucleotide base. Nicotinate mononucleotide (NaMN):base phosphoribosyltransferases (CobT) synthesize α-linked riboside monophosphates from diverse nucleotide base substrates (e.g., benzimidazoles, purin ...

    Cobamide diversity arises from the nature of the nucleotide base. Nicotinate mononucleotide (NaMN):base phosphoribosyltransferases (CobT) synthesize α-linked riboside monophosphates from diverse nucleotide base substrates (e.g., benzimidazoles, purines, phenolics) that are incorporated into cobamides.


    Organizational Affiliation

    Department of Bacteriology, University of Wisconsin, Madison, WI, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
A, B
356Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 3 
Gene Names: cobT
EC: 2.4.2.21
Find proteins for Q05603 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q05603
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCR
Query on PCR

Download SDF File 
Download CCD File 
A, B
P-CRESOL
C7 H8 O
IWDCLRJOBJJRNH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.664α = 90.00
b = 70.965β = 91.08
c = 88.400γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data collection
HKL-3000data scaling
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release