1KC7

Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis

Herzberg, O.Chen, C.C.Liu, S.Tempczyk, A.Howard, A.Wei, M.Ye, D.Dunaway-Mariano, D.

(2002) Biochemistry 41: 780-787

  • DOI: 10.1021/bi011799+
  • Primary Citation of Related Structures:  
    1KBL, 1KC7

  • PubMed Abstract: 
  • Crystals of pyruvate phosphate dikinase in complex with a substrate analogue inhibitor, phosphonopyruvate (K(i) = 3 microM), have been obtained in the presence of Mg(2+). The structure has been determined and refined at 2.2 A resolution, revealing that the Mg(2+)-bound phosphonopyruvate binds in the alpha/beta-barrel's central channel, at the C-termini of the beta-strands ...

    Crystals of pyruvate phosphate dikinase in complex with a substrate analogue inhibitor, phosphonopyruvate (K(i) = 3 microM), have been obtained in the presence of Mg(2+). The structure has been determined and refined at 2.2 A resolution, revealing that the Mg(2+)-bound phosphonopyruvate binds in the alpha/beta-barrel's central channel, at the C-termini of the beta-strands. The mode of binding resembles closely the previously proposed PEP substrate binding mode, inferred by the homology of the structure (but not sequence homology) to pyruvate kinase. Kinetic analysis of site-directed mutants, probing residues involved in inhibitor binding, showed that all mutations resulted in inactivation, confirming the key role that these residues play in catalysis. Comparison between the structure of the PPDK-phosphonopyruvate complex and the structures of two complexes of pyruvate kinase, one with Mg(2+)-bound phospholactate and the other with Mg(2+)-oxalate and ATP, revealed that the two enzymes share some key features that facilitate common modes of substrate binding. There are also important structural differences; most notably, the machinery for acid/base catalysis is different.


    Related Citations: 
    • SWIVELING-DOMAIN MECHANISM FOR ENZYMATIC PHOSPHOTRANSFER BETWEEN REMOTE REACTION SITES
      Herzberg, O., Chen, C.C.H., Kapadia, G., Mcguire, M., Carroll, L.J., Noh, S.J., Dunaway-Mariano, D.
      (1996) Proc Natl Acad Sci U S A 93: 2652
    • Location of the Phosphate Binding Site within Clostridium Symbiosum Pyruvate Phosphate dikinase
      Mcguire, M., Huang, K., Kapadia, G., Herzberg, O., Dunaway-Mariano, D.
      (1998) Biochemistry 37: 13463
    • Identification of Domain-Domain Docking Sites within Clostridium Symbiosum Pyruvate Phosphate Dikinase by Amino Acid Replacement
      Wei, M., Li, Z., Ye, D., Herzberg, O., Dunaway-Mariano, D.
      (2000) J Biol Chem 275: 41156

    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA. osnat@carb.nist.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pyruvate phosphate dikinaseA873[Clostridium] symbiosumMutation(s): 0 
Gene Names: ppdK
EC: 2.7.9.1
Find proteins for P22983 (Clostridium symbiosum)
Explore P22983 
Go to UniProtKB:  P22983
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPR
Query on PPR

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHONOPYRUVATE
C3 H5 O6 P
CHDDAVCOAOFSLD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPRKi:  3000   nM  Binding MOAD
PPRKi :  3000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.21α = 90
b = 58.42β = 94.99
c = 102.55γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance