4KQF

Crystal structure of CobT E174A complexed with adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

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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: 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. Structural investigations of two members of the CobT family of enzymes in complex with various substrate bases as well as in vivo and vitro activity analyses of enzyme variants were performed to elucidate the roles of key amino acid residues important for substrate recognition. Results of in vitro and in vivo studies of active-site variants of the Salmonella enterica CobT (SeCobT) enzyme suggest that a catalytic base may not be required for catalysis. This idea is supported by the analyses of crystal structures that show that two glutamate residues function primarily to maintain an active conformation of the enzyme. In light of these findings, we propose that proper positioning of the substrates in the active site triggers the attack at the C1 ribose of NaMN. Whether or not a catalytic base is needed for function is discussed within the framework of the in vitro analysis of the enzyme activity. Additionally, structure-guided site-directed mutagenesis of SeCobT broadened its substrate specificity to include phenolic bases, revealing likely evolutionary changes needed to increase cobamide diversity, and further supporting the proposed mechanism for the phosphoribosylation of phenolic substrates. Results of this study uncover key residues in the CobT enzyme that contribute to the diversity of cobamides in nature.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase356Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
Gene Names: cobTSTM2016
EC: 2.4.2.21
UniProt
Find proteins for Q05603 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q05603 
Go to UniProtKB:  Q05603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05603
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.488α = 90
b = 89.059β = 90
c = 46.759γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SADABSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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