Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 72.55 kDa 
• Atom Count: 5686 
• Modelled Residue Count: 633 
• Deposited Residue Count: 648 
• Unique protein chains: 1

2XZ9

CRYSTAL STRUCTURE FROM THE PHOSPHOENOLPYRUVATE-BINDING DOMAIN OF ENZYME I IN COMPLEX WITH PYRUVATE FROM THE THERMOANAEROBACTER TENGCONGENSIS PEP-SUGAR PHOSPHOTRANSFERASE SYSTEM (PTS)

• PDB DOI: 10.2210/pdb2XZ9/pdb

• Classification: TRANSFERASE
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-11-24 Released: 2011-06-15 
• Deposition Author(s): Oberholzer, A.E., Waltersperger, S.M., Schneider, P., Baumann, U., Erni, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Phosphoenolpyruvate: Sugar Phosphotransferase System from the Hyperthermophilic Thermoanaerobacter Tengcongensis.

Navdaeva, V., Zurbriggen, A., Waltersperger, S.M., Schneider, P., Oberholzer, A.E., Bahler, P., Bachler, C., Grieder, A., Baumann, U., Erni, B.

(2011) Biochemistry 50: 1184

• PubMed: 21250658 
• DOI: 10.1021/bi101721f
• Primary Citation of Related Structures:  
  2XZ7, 2XZ9


• PubMed Abstract: 
  

Thermoanaerobacter tengcongensis is a thermophilic eubacterium that has a phosphoenolpyruvate (PEP) sugar phosphotransferase system (PTS) of 22 proteins. The general PTS proteins, enzyme I and HPr, and the transporters for N-acetylglucosamine (EIICB(GlcNAc)) and fructose (EIIBC(Fru)) have thermal unfolding transitions at ∼90 °C and a temperature optimum for in vitro sugar phosphotransferase activity of 65 °C. The phosphocysteine of a EIICB(GlcNAc) mutant is unusually stable at room temperature with a t(1/2) of 60 h. The PEP binding C-terminal domain of enzyme I (EIC) forms a metastable covalent adduct with PEP at 65 °C. Crystallization of this adduct afforded the 1.68 Å resolution structure of EIC with a molecule of pyruvate in the active site. We also report the 1.83 Å crystal structure of the EIC-PEP complex. The comparison of the two structures with the apo form and with full-length EI shows differences between the active site side chain conformations of the PEP and pyruvate states but not between the pyruvate and apo states. In the presence of PEP, Arg465 forms a salt bridge with the phosphate moiety while Glu504 forms salt bridges with Arg186 and Arg195 of the N-terminal domain of enzyme I (EIN), which stabilizes a conformation appropriate for the in-line transfer of the phosphoryl moiety from PEP to His191. After transfer, Arg465 swings 4.8 Å away to form an alternative salt bridge with the carboxylate of Glu504. Glu504 loses the grip of Arg186 and Arg195, and the EIN domain can swing away to hand on the phosphoryl group to the phosphoryl carrier protein HPr.

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Organizational Affiliation: 

Department for Chemistry and Biochemistry, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)	A, B	324	Caldanaerobacter subterraneus subsp. tengcongensis	Mutation(s): 0  EC: 2.7.3.9
UniProt
Find proteins for Q8R7R4 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8R7R4  Go to UniProtKB:  Q8R7R4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYR	D [auth A], F [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.113	α = 90
b = 79.525	β = 90
c = 156.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-24 
• Released Date: 2011-06-15 
Deposition Author(s): Oberholzer, A.E., Waltersperger, S.M., Schneider, P., Baumann, U., Erni, B.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance