2DDO

Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK gene at 2.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.

Safo, M.K.Musayev, F.N.di Salvo, M.L.Hunt, S.Claude, J.B.Schirch, V.

(2006) J Bacteriol 188: 4542-4552

  • DOI: https://doi.org/10.1128/JB.00122-06
  • Primary Citation of Related Structures:  
    2DDM, 2DDO, 2DDW

  • PubMed Abstract: 

    The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, 800 E. Leigh St., Virginia Commonwealth University, Richmond, VA 23219, USA. msafo@mail2.vcu.edu


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxine kinase
A, B
283Escherichia coliMutation(s): 0 
Gene Names: PdxK
EC: 2.7.1.35
UniProt
Find proteins for P40191 (Escherichia coli (strain K12))
Explore P40191 
Go to UniProtKB:  P40191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40191
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.128α = 90
b = 74.356β = 90
c = 107.21γ = 90
Software Package:
Software NamePurpose
CNSrefinement
bioteXdata reduction
bioteXdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description