This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2var

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

Structural highlights

2var is a 3 chain structure with sequence from Saccharolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KDGK_SACS2 Involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase.,Potter JA, Kerou M, Lamble HJ, Bull SD, Hough DW, Danson MJ, Taylor GL Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1283-7. Epub 2008, Nov 18. PMID:19018105^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B. The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem J. 2005 Sep 1;390(Pt 2):529-40. PMID:15869466 doi:http://dx.doi.org/10.1042/BJ20041711
↑ Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett. 2005 Dec 19;579(30):6865-9. Epub 2005 Dec 1. PMID:16330030 doi:http://dx.doi.org/10.1016/j.febslet.2005.11.028
↑ Kim S, Lee SB. Characterization of Sulfolobus solfataricus 2-keto-3-deoxy-D-gluconate kinase in the modified Entner-Doudoroff pathway. Biosci Biotechnol Biochem. 2006 Jun;70(6):1308-16. PMID:16794308 doi:http://dx.doi.org/10.1271/bbb.50566
↑ Potter JA, Kerou M, Lamble HJ, Bull SD, Hough DW, Danson MJ, Taylor GL. The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase. Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1283-7. Epub 2008, Nov 18. PMID:19018105 doi:10.1107/S0907444908036111

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2var"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2-KETO-3-DEOXYGLUCONATE KINASE COMPLEXED WITH 2-KETO-3-DEOXYGLUCONATE==
-<StructureSection load='2var' size='340' side='right' caption='[[2var]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+==Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate==
+<StructureSection load='2var' size='340' side='right'caption='[[2var]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2var]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VAR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2var]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VAR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=KDF:3-DEOXY-ALPHA-D-ERYTHRO-HEX-2-ULOFURANOSONIC+ACID'>KDF</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v78|2v78]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=KDF:3-DEOXY-ALPHA-D-ERYTHRO-HEX-2-ULOFURANOSONIC+ACID'>KDF</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructokinase Fructokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.4 2.7.1.4] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2var FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2var OCA], [https://pdbe.org/2var PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2var RCSB], [https://www.ebi.ac.uk/pdbsum/2var PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2var ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2var FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2var OCA], [http://pdbe.org/2var PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2var RCSB], [http://www.ebi.ac.uk/pdbsum/2var PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KDGK_SULSO KDGK_SULSO]] Involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively.<ref>PMID:15869466</ref> <ref>PMID:16330030</ref> <ref>PMID:16794308</ref>
+[https://www.uniprot.org/uniprot/KDGK_SACS2 KDGK_SACS2] Involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively.<ref>PMID:15869466</ref> <ref>PMID:16330030</ref> <ref>PMID:16794308</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/va/2var_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/va/2var_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 35091]]
+[[Category: Large Structures]]
-[[Category: Fructokinase]]
+[[Category: Saccharolobus solfataricus]]
-[[Category: Bull, S D]]
+[[Category: Bull SD]]
-[[Category: Danson, M J]]
+[[Category: Danson MJ]]
-[[Category: Hough, D W]]
+[[Category: Hough DW]]
-[[Category: Kerou, M]]
+[[Category: Kerou M]]
-[[Category: Lamble, H J]]
+[[Category: Lamble HJ]]
-[[Category: Potter, J A]]
+[[Category: Potter JA]]
-[[Category: Taylor, G L]]
+[[Category: Taylor GL]]
-[[Category: Theodossis, A]]
+[[Category: Theodossis A]]
-[[Category: 2- keto-3-deoxygluconate kinase]]
-[[Category: 2- keto-3-deoxygluconate kinasekinase]]
-[[Category: Kinase]]
-[[Category: Pfkb family carbohydrate kinase]]
-[[Category: Sulfolobus solfataricus]]
-[[Category: Transferase]]

2var

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox