2var: Difference between revisions

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-{{Seed}}
-[[Image:2var.png|left|200px]]
-<!--
+==Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate==
-The line below this paragraph, containing "STRUCTURE_2var", creates the "Structure Box" on the page.
+<StructureSection load='2var' size='340' side='right'caption='[[2var]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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='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>
-{{STRUCTURE_2var|  PDB=2var  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[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>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2var ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2-KETO-3-DEOXYGLUCONATE KINASE COMPLEXED WITH 2-KETO-3-DEOXYGLUCONATE===
+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<ref>PMID:19018105</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2var" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-VAR is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAR OCA].
+*[[Fructokinase|Fructokinase]]
-[[Category: Fructokinase]]
+== References ==
-[[Category: Sulfolobus solfataricus]]
+<references/>
-[[Category: Bull, S D.]]
+__TOC__
-[[Category: Danson, M J.]]
+</StructureSection>
-[[Category: Hough, D W.]]
+[[Category: Large Structures]]
-[[Category: Kerou, M.]]
+[[Category: Saccharolobus solfataricus]]
-[[Category: Lamble, H J.]]
+[[Category: Bull SD]]
-[[Category: Potter, J A.]]
+[[Category: Danson MJ]]
-[[Category: Taylor, G L.]]
+[[Category: Hough DW]]
-[[Category: Theodossis, A.]]
+[[Category: Kerou M]]
-[[Category: 2- keto-3-deoxygluconate kinase]]
+[[Category: Lamble HJ]]
-[[Category: 2- keto-3-deoxygluconate kinasekinase]]
+[[Category: Potter JA]]
-[[Category: Kinase]]
+[[Category: Taylor GL]]
-[[Category: Pfkb family carbohydrate kinase]]
+[[Category: Theodossis A]]
-[[Category: Sulfolobus solfataricus]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 11 20:22:49 2009''