2VAR | pdb_00002var

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

PDB DOI: https://doi.org/10.2210/pdb2VAR/pdb

Classification: TRANSFERASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-04 Released: 2007-10-02
Deposition Author(s): Potter, J.A., Theodossis, A., Kerou, M., Lamble, H.J., Bull, S.D., Hough, D.W., Danson, M.J., Taylor, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 19018105 Search on PubMed
DOI: https://doi.org/10.1107/S0907444908036111
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 108.39 kDa
Atom Count: 8,064
Modeled Residue Count: 933
Deposited Residue Count: 939
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FRUCTOKINASE	A, B, C	313	Saccharolobus solfataricus	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97U29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C]	F [auth A], J [auth B], N [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C]	G [auth A], K [auth B], O [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C]
KDF Query on KDF Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C]	E [auth A], I [auth B], M [auth C]	3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid C₆ H₁₀ O₆ RCUMQJPRQWRUNN-MRKVFDINSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C]
KDG Query on KDG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C]	D [auth A], H [auth B], L [auth C]	2-KETO-3-DEOXYGLUCONATE C₆ H₁₀ O₆ WPAMZTWLKIDIOP-WVZVXSGGSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.218 (Depositor), 0.217 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.553	α = 90
b = 104.553	β = 90
c = 420.782	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-02

Deposition Author(s):

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