4UXD | pdb_00004uxd

2-keto 3-deoxygluconate aldolase from Picrophilus torridus

• PDB DOI: https://doi.org/10.2210/pdb4UXD/pdb

• Classification: LYASE
• Organism(s): Picrophilus oshimae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-22 Released: 2015-09-30 
• Deposition Author(s): Priftis, A., Zaitsev, V., Reher, M., Johnsen, U., Danson, M.J., Taylor, G.L., Schoenheit, P., Crennell, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate.

Zaitsev, V., Johnsen, U., Reher, M., Ortjohann, M., Taylor, G.L., Danson, M.J., Schonheit, P., Crennell, S.J.

(2018) Biochemistry 57: 3797-3806

• PubMed: 29812914 
• DOI: https://doi.org/10.1021/acs.biochem.8b00535
• Primary Citation Related Structures: 
  4UXD, 6G3Z


• PubMed Abstract: 
  

  The thermoacidophilic archaea Picrophilus torridus and Sulfolobus solfataricus catabolize glucose via a nonphosphorylative Entner-Doudoroff pathway and a branched Entner-Doudoroff pathway, respectively. Key enzymes for these Entner-Doudoroff pathways are the aldolases, 2-keto-3-deoxygluconate aldolase (KDG-aldolase) and 2-keto-3-deoxy-6-phosphogluconate aldolase [KD(P)G-aldolase]. KDG-aldolase from P. torridus (Pt-KDG-aldolase) is highly specific for the nonphosphorylated substrate, 2-keto-3-deoxygluconate (KDG), whereas KD(P)G-aldolase from S. solfataricus [Ss-KD(P)G-aldolase] is an enzyme that catalyzes the cleavage of both KDG and 2-keto-3-deoxy-6-phosphogluconate (KDPG), with a preference for KDPG. The structural basis for the high specificity of Pt-KDG-aldolase for KDG as compared to the more promiscuous Ss-KD(P)G-aldolase has not been analyzed before. In this work, we report the elucidation of the structure of Ss-KD(P)G-aldolase in complex with KDPG at 2.35 Å and that of KDG-aldolase from P. torridus at 2.50 Å resolution. By superimposition of the active sites of the two enzymes, and subsequent site-directed mutagenesis studies, a network of four amino acids, namely, Arg106, Tyr132, Arg237, and Ser241, was identified in Ss-KD(P)G-aldolase that interact with the negatively charged phosphate group of KDPG, thereby increasing the affinity of the enzyme for KDPG. This KDPG-binding network is absent in Pt-KDG-aldolase, which explains the low catalytic efficiency of KDPG cleavage.

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Organizational Affiliation: 
• Biomolecular Sciences , University of St Andrews , St Andrews , Fife KY16 9ST , U.K.
Institut für Allgemeine Mikrobiologie , Christian-Albrechts-Universität , D-24118 Kiel , Germany.
Department of Biology & Biochemistry , University of Bath , Bath BA2 7AY , U.K.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 138.88 kDa 
• Atom Count: 9,319 
• Modeled Residue Count: 1,096 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE	A, B, C, D	297	Picrophilus oshimae	Mutation(s): 0  EC: 4.1.2.51 (PDB Primary Data), 4.1.2.14 (PDB Primary Data), 4.1.2.21 (PDB Primary Data), 4.1.2 (UniProt)
UniProt
Find proteins for Q6KZI8 (Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / KAW 2/3)) Explore Q6KZI8  Go to UniProtKB:  Q6KZI8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	V [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	S [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	AA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], W [auth C], X [auth C], Y [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	BA [auth D], CA [auth D], H [auth A], U [auth C], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	G [auth A], GA [auth D], O [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.954	α = 90
b = 100.159	β = 90
c = 154.609	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Priftis, A., Zaitsev, V., Reher, M., Johnsen, U., Danson, M.J., Taylor, G.L., Schoenheit, P., Crennell, S.J.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references
• Version 1.2: 2018-07-11
  Changes: Data collection, Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description