4KQH

Crystal structure of CobT E317A

• PDB DOI: https://doi.org/10.2210/pdb4KQH/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-15 Released: 2014-03-12 
• Deposition Author(s): Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

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

• PubMed: 24121107 
• DOI: https://doi.org/10.1016/j.bbagen.2013.09.038
• Primary Citation of Related Structures:  
  4KQF, 4KQG, 4KQH, 4KQI, 4KQJ, 4KQK


• 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, purines, phenolics) that are incorporated into cobamides.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.94 kDa 
• Atom Count: 2,696 
• Modelled Residue Count: 336 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase	A	356	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1  Gene Names: cobT, STM2016 EC: 2.4.2.21
UniProt
Find proteins for Q05603 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q05603  Go to UniProtKB:  Q05603

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.417	α = 90
b = 89.966	β = 90
c = 47.013	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Chan, C.H., Newmister, S.A., Taylor, K.C., Claas, K.R., Rayment, I., Escalante-Semerena, J.C.

Revision History  

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