Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 65.13 kDa 
• Atom Count: 5046 
• Modelled Residue Count: 576 
• Deposited Residue Count: 576 
• Unique protein chains: 1

2NUW

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

• PDB DOI: 10.2210/pdb2NUW/pdb

• Classification: LYASE
• Organism(s): Sulfolobus acidocaldarius DSM 639
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-10 Released: 2007-04-10 
• Deposition Author(s): van Eerde, A., Dijkstra, B.W.

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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 

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

• PubMed: 17176250 
• DOI: 10.1042/BJ20061419
• Primary Citation of Related Structures:  
  2NUW, 2NUX, 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-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.

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Organizational Affiliation: 

Laboratory of Microbiology, Wageningen University, 6703 CT Wageningen, The Netherlands. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase	A, B	288	Sulfolobus acidocaldarius DSM 639	Mutation(s): 0  Gene Names: Saci_0225 EC: 4.1.2.14 (PDB Primary Data), 4.1.2.55 (UniProt)
UniProt
Find proteins for Q4JC35 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4JC35  Go to UniProtKB:  Q4JC35

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 108.16	α = 90
b = 108.16	β = 90
c = 171.852	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-10 
• Released Date: 2007-04-10 
Deposition Author(s): van Eerde, A., Dijkstra, B.W.

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