1X6U

KDO8P synthase in it's binary complex with the product KDO8P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structures of Escherichia coli KDO8P Synthase Complexes Reveal the Source of Catalytic Irreversibility

Vainer, R.Belakhov, V.Rabkin, E.Baasov, T.Adir, N.

(2005) J Mol Biol 351: 641-652

  • DOI: 10.1016/j.jmb.2005.06.021
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial ...

    The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial modes of ligand binding in KDO8PS binary complexes by X-ray crystallography. Structures of the apo-enzyme and of binary complexes with the substrate PEP, the product KDO8P and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate (1dA5P) were obtained. The KDO8PS active site resembles an irregular funnel with positive electrostatic potential situated at the bottom of the PEP-binding sub-site, which is the primary attractive force towards negatively charged phosphate moieties of all ligands. The structures of the ligand-free apo-KDO8PS and the binary complex with the product KDO8P visualize for the first time the role of His202 as an active-site gate. Examination of the crystal structures of KDO8PS with the KDO8P or 1dA5P shows these ligands bound to the enzyme in the PEP-binding sub-site, and not as expected to the A5P sub-site. Taken together, the structures presented here strengthen earlier evidence that this enzyme functions predominantly through positional catalysis, map out the roles of active-site residues and provide evidence that explains the total lack of catalytic reversibility.


    Organizational Affiliation

    Department of Chemistry and Institute of Catalysis, Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-dehydro-3-deoxyphosphooctonate aldolaseA284Escherichia coliMutation(s): 0 
Gene Names: kdsA
EC: 2.5.1.55
Find proteins for P0A715 (Escherichia coli (strain K12))
Explore P0A715 
Go to UniProtKB:  P0A715
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DO8
Query on DO8

Download CCD File 
A
3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid
C8 H15 O11 P
IZZNRKJLBIYBJN-HXUQBWEZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DO8Ki :  600000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.53α = 90
b = 118.53β = 90
c = 118.53γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary