1GG0

CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate.

Wagner, T.Kretsinger, R.H.Bauerle, R.Tolbert, W.D.

(2000) J Mol Biol 301: 233-238

  • DOI: 10.1006/jmbi.2000.3956
  • Primary Citation of Related Structures:  
    1GG0

  • PubMed Abstract: 
  • The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDOPS) from Escherichia coli was determined by molecular replacement using coordinates given to us by Radaev and co-workers prior to publication. The KDOPS crystals reported by Radaev et al ...

    The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDOPS) from Escherichia coli was determined by molecular replacement using coordinates given to us by Radaev and co-workers prior to publication. The KDOPS crystals reported by Radaev et al. were grown in the presence of 1.4 M (NH(4))(2)SO(4) and 0.4 M (K/H)(3)PO(4). They are in the cubic space group I23 (a=228.6 A) with a tetramer in the asymmetric unit; the structure has been refined with data to 2.4 A. Our crystals of E. coli KDOPS, grown in 24 % (w/v) polyethylene glycol (PEG) 1500 in the presence of the substrates, 2-phosphoenolpyruvate (PEP) and d-arabinose-5-phosphate (A5P), are also in space group I23 (a=118.2 A), with one subunit in the asymmetric unit. The medium of crystallization, 1.8 M SO(4)/PO(4) versus 24 % PEG, does not significantly affect the conformation of KDOPS. The inter-monomer contacts in both structures are the same. The beta(8)/alpha(8) loop (residues 246 to 251) situated near the entrance to the active site is not seen in the 229 A structure but can be traced in the 118 A structure. Most significantly, Radaev et al. interpreted two SO(4)/PO(4) sites in the 229 A structure as marking the phosphate positions of the substrates, PEP and A5P, after the precedent of DAHPS. In the 118 A structure the inner of these two SO(4)/PO(4) peaks is present at the same position as in the 229 A structure of KDOPS. The outer phosphate peak in the 118 A KDOPS is 3.7 A from the outer SO(4)/PO(4) peak in the 229 A structure and is within hydrogen bonding distance of Arg63 of the same subunit and Arg120 of another subunit. Based on the precedent of the d-erythrose-4-phosphate (E4P) modeled in the active site of DAHPS, we have modeled PEP and A5P in KDOPS and compared the coordination of PEP and A5P in KDOPS with that of PEP and E4P in DAHPS.


    Related Citations: 
    • Structure and mechanism of 3-deoxy-D-manno-octulosonate-8-phosphate synthase
      Radaev, S., Dastidar, P., Patel, M., Woodard, R.W., Gatti, D.L.
      (2000) J Biol Chem 275: 9476
    • Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli
      Tolbert, W.D., Moll, J.R., Bauerle, R., Kretsinger, R.H.
      (1996) Proteins 24: 407

    Organizational Affiliation

    Department of Biology, University of Virginia, Charlottesville, VA, 22903-2477, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASEA284Escherichia coliMutation(s): 0 
EC: 4.1.2.16 (PDB Primary Data), 2.5.1.55 (UniProt)
UniProt
Find proteins for P0A715 (Escherichia coli (strain K12))
Explore P0A715 
Go to UniProtKB:  P0A715
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.167α = 90
b = 118.167β = 90
c = 118.167γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-04
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description