2F7K

Crystal Structure of Human Pyridoxal Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.250 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human pyridoxal kinase

Cao, P.Gong, Y.Tang, L.Leung, Y.C.Jiang, T.

(2006) J Struct Biol 154: 327-332

  • DOI: 10.1016/j.jsb.2006.02.008
  • Primary Citation of Related Structures:  
    2F7K

  • PubMed Abstract: 
  • Pyridoxal kinase, a member of the ribokinase superfamily, catalyzes the ATP-dependent phosphorylation reaction of vitamin B6 and is an essential enzyme in the formation of pyridoxal-5'-phosphate, a key cofactor for over 100 enzymes. Pyridoxal kinase is thus regarded as a potential target for pharmacological agents ...

    Pyridoxal kinase, a member of the ribokinase superfamily, catalyzes the ATP-dependent phosphorylation reaction of vitamin B6 and is an essential enzyme in the formation of pyridoxal-5'-phosphate, a key cofactor for over 100 enzymes. Pyridoxal kinase is thus regarded as a potential target for pharmacological agents. In this paper, we report the 2.8 angstroms crystal structure of human pyridoxal kinase (HPLK) expressed in Escherichia coli. The diffraction data revealed unexpected merohedral perfect twinning along the crystallographic c axis. Taking perfect twinning into account, the structure in dimeric form was well refined according to the CNS program. Structure comparison reveals that the key 12-residue peptide over the active site in HPLK is a beta-strand/loop/beta-strand flap, while the corresponding peptide in sheep brain enzyme adopts a loop conformation. Moreover, HPLK possesses a more hydrophobic ATP-binding pocket. This structure will facilitate further biochemical studies and structure-based design of drugs related to pyridoxal kinase.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyridoxal kinaseA, B327Homo sapiensMutation(s): 0 
Gene Names: PDXKC21orf124C21orf97PKHPNKPRED79
EC: 2.7.1.35
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.250 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.5α = 90
b = 52.5β = 90
c = 301γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
CrystalCleardata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance