1rk2: Difference between revisions

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-[[Image:1rk2.jpg|left|200px]]
- {{Structure
+==E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121==
-|PDB= 1rk2 |SIZE=350|CAPTION= <scene name='initialview01'>1rk2</scene>, resolution 2.25&Aring;
+<StructureSection load='1rk2' size='340' side='right'caption='[[1rk2]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=RIB:RIBOSE'>RIB</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>
+<table><tr><td colspan='2'>[[1rk2]] is a 4 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=1RK2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RK2 FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Ribokinase Ribokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.15 2.7.1.15]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
-|GENE= RBSK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></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=1rk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rk2 OCA], [https://pdbe.org/1rk2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rk2 RCSB], [https://www.ebi.ac.uk/pdbsum/1rk2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rk2 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/1rk2_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=1rk2 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 COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121'''
+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 1rk2" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Ribokinase 3D structures|Ribokinase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-RK2 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=1RK2 OCA].
+__TOC__
+</StructureSection>
-==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: ADP]]
-[[Category: ALF]]
-[[Category: MG]]
-[[Category: RIB]]
-[[Category: carbohydrate kinase]]
-[[Category: domain re-arrangement]]
-[[Category: induced fit]]
-[[Category: ribose]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:29:13 2008''