2HWG

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 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 10.1073/pnas.0607587103
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoenolpyruvate-protein phosphotransferaseA, B575Escherichia coliMutation(s): 19 
Gene Names: ptsI
EC: 2.7.3.9
Find proteins for P08839 (Escherichia coli (strain K12))
Explore P08839 
Go to UniProtKB:  P08839
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXL
Query on OXL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
NEP
Query on NEP
A, BL-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OXLKi :  280000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • 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