2NUW

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases

Wolterink-van Loo, S.van Eerde, A.Siemerink, M.A.J.Akerboom, J.Dijkstra, B.W.van der Oost, J.

(2007) Biochem J 403: 421-430

  • DOI: 10.1042/BJ20061419
  • Primary Citation of Related Structures:  
    2NUX, 2NUW, 2NUY

  • PubMed Abstract: 
  • Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present study, the genomes of Sulfolobus species were screened for aldolases. Two new KDGA [2-keto-3-deoxygluconate (2-o ...

    Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present study, the genomes of Sulfolobus species were screened for aldolases. Two new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were found to have biochemical properties similar to the previously characterized S. solfataricus KDGA, including the condensation of pyruvate and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The crystal structure of S. acidocaldarius KDGA revealed the presence of a novel phosphate-binding motif that allows the formation of multiple hydrogen-bonding interactions with the acceptor substrate, and enables high activity with glyceraldehyde 3-phosphate. Activity analyses with unnatural substrates revealed that these three KDGAs readily accept aldehydes with two to four carbon atoms, and that even aldoses with five carbon atoms are accepted to some extent. Water-mediated interactions permit binding of substrates in multiple conformations in the spacious hydrophilic binding site, and correlate with the observed broad substrate specificity.


    Organizational Affiliation

    Laboratory of Microbiology, Wageningen University, 6703 CT Wageningen, The Netherlands. suzanne.vanloo@wur.nl



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolaseA, B288Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
Gene Names: Saci_0225
EC: 4.1.2.14 (PDB Primary Data), 4.1.2.55 (UniProt)
Find proteins for Q4JC35 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4JC35 
Go to UniProtKB:  Q4JC35
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.16α = 90
b = 108.16β = 90
c = 171.852γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description