1JXI

4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium complexed with 4-Amino-5-hydroxymethyl-2-methylpyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.230 

Starting Model: other
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.

Cheng, G.Bennett, E.M.Begley, T.P.Ealick, S.E.

(2002) Structure 10: 225-235

  • DOI: https://doi.org/10.1016/s0969-2126(02)00708-6
  • Primary Citation of Related Structures:  
    1JXH, 1JXI

  • PubMed Abstract: 

    The crystal structures of Salmonella typhimurium 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) and its complex with substrate HMP have been determined. HMPP kinase catalyzes two separate ATP-dependent phosphorylation reactions and is an essential enzyme in the thiamin biosynthetic pathway. HMPP kinase is a homodimer with one active site per monomer and is structurally homologous to members of the ribokinase family. A comparison of the structure of HMPP kinase with other members of the ribokinase family suggests an evolutionary progression. Modeling studies suggest that HMPP kinase catalyzes both of its phosphorylation reactions using in-line displacement mechanisms. We propose that the active site accommodates the two separate reactions by providing two different binding modes for the phosphate group of HMP phosphate.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOMETHYLPYRIMIDINE KINASE
A, B
288Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: thiD
EC: 2.7.4.7
UniProt
Find proteins for P55882 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P55882 
Go to UniProtKB:  P55882
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55882
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.75α = 90
b = 77.75β = 90
c = 183.49γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description