1DIK | pdb_00001dik

PYRUVATE PHOSPHATE DIKINASE

• PDB DOI: https://doi.org/10.2210/pdb1DIK/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): [Clostridium] symbiosum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-12-06 Released: 1996-04-03 
• Deposition Author(s): Herzberg, O., Chen, C.C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.

Herzberg, O., Chen, C.C., Kapadia, G., McGuire, M., Carroll, L.J., Noh, S.J., Dunaway-Mariano, D.

(1996) Proc Natl Acad Sci U S A 93: 2652-2657

• PubMed: 8610096 
• DOI: https://doi.org/10.1073/pnas.93.7.2652
• Primary Citation Related Structures: 
  1DIK


• PubMed Abstract: 
  

  The crystal structure of pyruvate phosphate dikinase, a histidyl multiphosphotransfer enzyme that synthesizes adenosine triphosphate, reveals a three-domain molecule in which the phosphohistidine domain is flanked by the nucleotide and the phosphoenolpyruvate/pyruvate domains, with the two substrate binding sites approximately 45 angstroms apart. The modes of substrate binding have been deduced by analogy to D-Ala-D-Ala ligase and to pyruvate kinase. Coupling between the two remote active sites is facilitated by two conformational states of the phosphohistidine domain. While the crystal structure represents the state of interaction with the nucleotide, the second state is achieved by swiveling around two flexible peptide linkers. This dramatic conformational transition brings the phosphocarrier residue in close proximity to phosphoenolpyruvate/pyruvate. The swiveling-domain paradigm provides an effective mechanism for communication in complex multidomain/multiactive site proteins.

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Organizational Affiliation: 
• Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, 20850, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 97.07 kDa 
• Atom Count: 7,161 
• Modeled Residue Count: 869 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE PHOSPHATE DIKINASE	A	874	[Clostridium] symbiosum	Mutation(s): 0  Gene Names: PPDK EC: 2.7.9.1
UniProt
Find proteins for P22983 (Clostridium symbiosum) Explore P22983  Go to UniProtKB:  P22983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.8	α = 90
b = 58.8	β = 94.8
c = 102	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-03 
Deposition Author(s): Herzberg, O., Chen, C.C.H.

Revision History  

• Version 1.0: 1996-04-03
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other