1RFU

Crystal structure of pyridoxal kinase complexed with ADP and PLP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational changes in the reaction of pyridoxal kinase

Li, M.-H.Kwok, F.Chang, W.-R.Liu, S.-Q.Lo, S.C.L.Zhang, J.-P.Jiang, T.Liang, D.-C.

(2004) J.BIOL.CHEM. 279: 17459-17465

  • DOI: 10.1074/jbc.M312380200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK e ...

    To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.


    Related Citations: 
    • Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily
      Li, M.-H.,Kwok, F.,Chang, W.-R.,Lau, C.-K.,Zhang, J.-P.,Lo, S.C.L.,Jiang, T.,Liang, D.-C.
      (2002) J.Biol.Chem. 277: 46385
    • Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain
      Li, M.-H.,Kwok, F.,An, X.-M.,Chang, W.-R.,Lau, C.-K.,Zhang, J.-P.,Liu, S.-Q.,Leung, Y.-C.,Jiang, T.,Liang, D.-C.
      (2002) Acta Crystallogr.,Sect.D 58: 1479


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pyridoxal kinase
A, B, C, D, E, F, G, H
312Ovis ariesMutation(s): 0 
Gene Names: PDXK (PKH)
EC: 2.7.1.35
Find proteins for P82197 (Ovis aries)
Go to Gene View: PDXK
Go to UniProtKB:  P82197
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.229 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 109.088α = 90.00
b = 109.088β = 90.00
c = 284.272γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance