2HWG | pdb_00002hwg

Structure of phosphorylated Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.284 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein.

Teplyakov, A.Lim, K.Zhu, P.P.Kapadia, G.Chen, C.C.Schwartz, J.Howard, A.Reddy, P.T.Peterkofsky, A.Herzberg, O.

(2006) Proc Natl Acad Sci U S A 103: 16218-16223

  • DOI: https://doi.org/10.1073/pnas.0607587103
  • Primary Citation Related Structures: 
    2HWG

  • PubMed Abstract: 

    Bacterial transport of many sugars, coupled to their phosphorylation, is carried out by the phosphoenolpyruvate (PEP):sugar phosphotransferase system and involves five phosphoryl group transfer reactions. Sugar translocation initiates with the Mg(2+)-dependent phosphorylation of enzyme I (EI) by PEP. Crystals of Escherichia coli EI were obtained by mixing the protein with Mg(2+) and PEP, followed by oxalate, an EI inhibitor. The crystal structure reveals a dimeric protein where each subunit comprises three domains: a domain that binds the partner PEP:sugar phosphotransferase system protein, HPr; a domain that carries the phosphorylated histidine residue, His-189; and a PEP-binding domain. The PEP-binding site is occupied by Mg(2+) and oxalate, and the phosphorylated His-189 is in-line for phosphotransfer to/from the ligand. Thus, the structure represents an enzyme intermediate just after phosphotransfer from PEP and before a conformational transition that brings His-189 approximately P in proximity to the phosphoryl group acceptor, His-15 of HPr. A model of this conformational transition is proposed whereby swiveling around an alpha-helical linker disengages the His domain from the PEP-binding domain. Assuming that HPr binds to the HPr-binding domain as observed by NMR spectroscopy of an EI fragment, a rotation around two linker segments orients the His domain relative to the HPr-binding domain so that His-189 approximately P and His-15 are appropriately stationed for an in-line phosphotransfer reaction.


  • Organizational Affiliation
    • Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.

Macromolecule Content 

  • Total Structure Weight: 129.34 kDa 
  • Atom Count: 9,102 
  • Modeled Residue Count: 1,144 
  • Deposited Residue Count: 1,150 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphoenolpyruvate-protein phosphotransferase
A, B
575Escherichia coliMutation(s): 19 
Gene Names: ptsI
EC: 2.7.3.9
UniProt
Find proteins for P08839 (Escherichia coli (strain K12))
Explore P08839 
Go to UniProtKB:  P08839
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08839
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.284 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.487α = 90
b = 94.084β = 90
c = 161.007γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection