Human Pyridoxal Kinase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.

Musayev, F.N.di Salvo, M.L.Ko, T.P.Gandhi, A.K.Goswami, A.Schirch, V.Safo, M.K.

(2007) Protein Sci 16: 2184-2194

  • DOI: https://doi.org/10.1110/ps.073022107
  • Primary Citation of Related Structures:  
    2YXT, 2YXU

  • PubMed Abstract: 

    Pyridoxal kinase catalyzes the transfer of a phosphate group from ATP to the 5' alcohol of pyridoxine, pyridoxamine, and pyridoxal. In this work, kinetic studies were conducted to examine monovalent cation dependence of human pyridoxal kinase kinetic parameters. The results show that hPLK affinity for ATP and PL is increased manyfold in the presence of K(+) when compared to Na(+); however, the maximal activity of the Na(+) form of the enzyme is more than double the activity in the presence of K(+). Other monovalent cations, Li(+), Cs(+), and Rb(+) do not show significant activity. We have determined the crystal structure of hPLK in the unliganded form, and in complex with MgATP to 2.0 and 2.2 A resolution, respectively. Overall, the two structures show similar open conformation, and likely represent the catalytically idle state. The crystal structure of the MgATP complex also reveals Mg(2+) and Na(+) acting in tandem to anchor the ATP at the active site. Interestingly, the active site of hPLK acts as a sink to bind several molecules of MPD. The features of monovalent and divalent metal cation binding, active site structure, and vitamin B6 specificity are discussed in terms of the kinetic and structural studies, and are compared with those of the sheep and Escherichia coli enzymes.

  • Organizational Affiliation

    Department of Medicinal Chemistry, School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal kinase
A, B
312Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O00764 (Homo sapiens)
Explore O00764 
Go to UniProtKB:  O00764
PHAROS:  O00764
GTEx:  ENSG00000160209 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00764
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
C6 H14 O2
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
D [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
O4 P
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.63α = 90
b = 115.286β = 90
c = 172.403γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CaspRmodel building
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description