2JG1

STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE with cofactor and substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase Implicate Domain Motions in Specificity and Mechanism.

Miallau, L.Hunter, W.N.Mcsweeney, S.M.Leonard, G.A.

(2007) J.Biol.Chem. 282: 19948

  • DOI: 10.1074/jbc.M701480200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High resolution structures of Staphylococcus aureus d-tagatose-6-phosphate kinase (LacC) in two crystal forms are herein reported. The structures define LacC in apoform, in binary complexes with ADP or the co-factor analogue AMP-PNP, and in a ternary ...

    High resolution structures of Staphylococcus aureus d-tagatose-6-phosphate kinase (LacC) in two crystal forms are herein reported. The structures define LacC in apoform, in binary complexes with ADP or the co-factor analogue AMP-PNP, and in a ternary complex with AMP-PNP and D-tagatose-6-phosphate. The tertiary structure of the LacC monomer, which is closely related to other members of the pfkB subfamily of carbohydrate kinases, is composed of a large alpha/beta core domain and a smaller, largely beta "lid." Four extended polypeptide segments connect these two domains. Dimerization of LacC occurs via interactions between lid domains, which come together to form a beta-clasp structure. Residues from both subunits contribute to substrate binding. LacC adopts a closed structure required for phosphoryl transfer only when both substrate and co-factor are bound. A reaction mechanism similar to that used by other phosphoryl transferases is proposed, although unusually, when both substrate and co-factor are bound to the enzyme two Mg(2+) ions are observed in the active site. A new motif of amino acid sequence conservation common to the pfkB subfamily of carbohydrate kinases is identified.


    Organizational Affiliation

    Macromolecular Crystallography Group, European Synchrotron Radiation Facility, 38043 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAGATOSE-6-PHOSPHATE KINASE
A, B, C, D
330Staphylococcus aureus (strain NCTC 8325)Mutation(s): 2 
Gene Names: lacC
EC: 2.7.1.144
Find proteins for P0A0B9 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0B9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TA6
Query on TA6

Download SDF File 
Download CCD File 
C
6-O-PHOSPHONO-BETA-D-TAGATOFURANOSE
C6 H13 O9 P
BGWGXPAPYGQALX-DPYQTVNSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.200α = 90.00
b = 97.090β = 90.00
c = 154.470γ = 90.00
Software Package:
Software NamePurpose
XPREPphasing
SHELXEphasing
SHELXDphasing
REFMACrefinement
SHARPmodel building
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance