3FHX

Crystal structure of D235A mutant of human pyridoxal kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase.

Gandhi, A.K.Ghatge, M.S.Musayev, F.N.Sease, A.Aboagye, S.O.di Salvo, M.L.Schirch, V.Safo, M.K.

(2009) Biochem Biophys Res Commun 381: 12-15

  • DOI: 10.1016/j.bbrc.2009.01.170
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pyridoxal kinase catalyzes the phosphorylation of pyridoxal (PL) to pyridoxal 5'-phosphate (PLP). A D235A variant shows 7-fold and 15-fold decreases in substrate affinity and activity, respectively. A D235N variant shows approximately 2-fold decrease ...

    Pyridoxal kinase catalyzes the phosphorylation of pyridoxal (PL) to pyridoxal 5'-phosphate (PLP). A D235A variant shows 7-fold and 15-fold decreases in substrate affinity and activity, respectively. A D235N variant shows approximately 2-fold decrease in both PL affinity and activity. The crystal structure of D235A (2.5 A) shows bound ATP, PL and PLP, while D235N (2.3 A) shows bound ATP and sulfate. These results document the role of Asp235 in PL kinase activity. The observation that the active site of PL kinase can accommodate both ATP and PLP suggests that formation of a ternary Enz.PLP.ATP complex could occur in the wild-type enzyme, consistent with severe MgATP substrate inhibition of PL kinase in the presence of PLP.


    Organizational Affiliation

    Department of Medicinal Chemistry, School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 East Leigh Street, Suite 212, Richmond VA 23219, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal kinaseA, B312Homo sapiensMutation(s): 1 
Gene Names: C21orf124C21orf97PDXKPKHPNKPRED79
EC: 2.7.1.35
Find proteins for O00764 (Homo sapiens)
Explore O00764 
Go to UniProtKB:  O00764
NIH Common Fund Data Resources
PHAROS  O00764
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PLP
Query on PLP

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B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
PXL
Query on PXL

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A, B
3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
C8 H9 N O3
RADKZDMFGJYCBB-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.224α = 90
b = 115.422β = 90
c = 168.898γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance