1rks: Difference between revisions

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-{{Seed}}
-[[Image:1rks.png|left|200px]]
-<!--
+==E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE==
-The line below this paragraph, containing "STRUCTURE_1rks", creates the "Structure Box" on the page.
+<StructureSection load='1rks' size='340' side='right'caption='[[1rks]], [[Resolution|resolution]] 2.40&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'>[[1rks]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKS 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]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>
-{{STRUCTURE_1rks|  PDB=1rks  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rks OCA], [https://pdbe.org/1rks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rks RCSB], [https://www.ebi.ac.uk/pdbsum/1rks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rks ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RBSK_ECOLI RBSK_ECOLI]
+== 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/rk/1rks_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=1rks ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme ribokinase phosphorylates ribose at O5* as the first step in its metabolism. The original X-ray structure of Escherichia coli ribokinase represented the ternary complex including ribose and ADP. Structures are presented here for the apo enzyme, as well as the ribose-bound state and four new ternary complex forms. Combined, the structures suggest that large and small conformational changes play critical roles in the function of this kinase. An initially open apo form can allow entry of the ribose substrate. After ribose binding, the active site lid is observed in a closed conformation, with the sugar trapped underneath. This closure and associated changes in the protein appear to assist ribokinase in recognition of the co-substrate ATP as the next step. Binding of the nucleotide brings about further, less dramatic adjustments in the enzyme structure. Additional small movements are almost certainly required during the phosphoryltransfer reaction. Evidence is presented that some types of movements of the lid are allowed in the ternary complex, which may be critical to the creation and breakdown of the transition state. Similar events are likely to take place during catalysis by other related carbohydrate kinases, including adenosine kinase.
-===E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE===
+Induced fit on sugar binding activates ribokinase.,Sigrell JA, Cameron AD, Mowbray SL J Mol Biol. 1999 Jul 30;290(5):1009-18. PMID:10438599<ref>PMID:10438599</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rks" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10438599}}, adds the Publication Abstract to the page
+*[[Ribokinase 3D structures|Ribokinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10438599 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10438599}}
+__TOC__
+</StructureSection>
-==About this Structure==
-RKS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKS OCA].
-==Reference==
-Induced fit on sugar binding activates ribokinase., Sigrell JA, Cameron AD, Mowbray SL, J Mol Biol. 1999 Jul 30;290(5):1009-18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10438599 10438599]
 [[Category: Escherichia coli]]
-[[Category: Ribokinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Cameron AD]]
-[[Category: Cameron, A D.]]
+[[Category: Mowbray SL]]
-[[Category: Mowbray, S L.]]
+[[Category: Sigrell JA]]
-[[Category: Sigrell, J A.]]
-[[Category: Carbohydrate kinase]]
-[[Category: Induced fit]]
-[[Category: Ribose]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:30:01 2008''