2VAR

Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view detailsBest fitted AMPClick on this verticalbar to view detailsBest fitted KDFClick on this verticalbar to view detailsBest fitted KDGClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

The Structure of Sulfolobus Solfataricus 2-Keto-3-Deoxygluconate Kinase.

Potter, J.A.Kerou, M.Lamble, H.J.Bull, S.D.Hough, D.W.Danson, M.J.Taylor, G.L.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1283

  • DOI: https://doi.org/10.1107/S0907444908036111
  • Primary Citation of Related Structures:  
    2V78, 2VAR

  • PubMed Abstract: 

    The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 353 K and utilizes an unusual promiscuous nonphosphorylative Entner-Doudoroff pathway to metabolize both glucose and galactose. It has been proposed that a part-phosphorylative Entner-Doudoroff pathway occurs in parallel in S. solfataricus, in which the 2-keto-3-deoxygluconate kinase (KDGK) is promiscuous for both glucose and galactose metabolism. Recombinant S. solfataricus KDGK protein was expressed in Escherichia coli, purified and crystallized in 0.1 M sodium acetate pH 4.1 and 1.4 M NaCl. The crystal structure of apo S. solfataricus KDGK was solved by molecular replacement to a resolution of 2.0 A and a ternary complex with 2-keto-3-deoxygluconate (KDGlu) and an ATP analogue was resolved at 2.1 A. The complex suggests that the structural basis for the enzyme's ability to phosphorylate KDGlu and 2-keto-3-deoxygalactonate (KDGal) is derived from a subtle repositioning of residues that are conserved in homologous nonpromiscuous kinases.


  • Organizational Affiliation

    Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FRUCTOKINASE
A, B, C
313Saccharolobus solfataricusMutation(s): 0 
EC: 2.7.1.4 (PDB Primary Data), 2.7.1.178 (UniProt)
UniProt
Find proteins for Q97U29 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97U29 
Go to UniProtKB:  Q97U29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97U29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
KDF
Query on KDF

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C]
3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid
C6 H10 O6
RCUMQJPRQWRUNN-MRKVFDINSA-N
KDG
Query on KDG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
L [auth C]
2-KETO-3-DEOXYGLUCONATE
C6 H10 O6
WPAMZTWLKIDIOP-WVZVXSGGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.553α = 90
b = 104.553β = 90
c = 420.782γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view detailsBest fitted AMPClick on this verticalbar to view detailsBest fitted KDFClick on this verticalbar to view detailsBest fitted KDGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Structure summary