1rkd: Difference between revisions

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-[[Image:1rkd.gif|left|200px]]
- {{Structure
+==E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP==
-|PDB= 1rkd |SIZE=350|CAPTION= <scene name='initialview01'>1rkd</scene>, resolution 1.84&Aring;
+<StructureSection load='1rkd' size='340' side='right'caption='[[1rkd]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AB1:Residues+Making+Direct+H+Bonds+w.+Adp'>AB1</scene>, <scene name='pdbsite=AB2:Residues+Making+Water-Mediated+H+Bonds+w.+Adp'>AB2</scene>, <scene name='pdbsite=AB3:Residues+Within+Van+Der+Waals+Distance+Of+Adp'>AB3</scene>, <scene name='pdbsite=RB1:Residues+Making+Direct+H+Bonds+w.+Ribose'>RB1</scene>, <scene name='pdbsite=RB2:Residues+Making+Water-Mediated+H+Bonds+w.+Ribose'>RB2</scene> and <scene name='pdbsite=RB3:Residues+Within+Van+Der+Waals+Distance+Of+Ribose'>RB3</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene>
+<table><tr><td colspan='2'>[[1rkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKD FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.84&#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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkd OCA], [https://pdbe.org/1rkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkd RCSB], [https://www.ebi.ac.uk/pdbsum/1rkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkd ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkd OCA], [http://www.ebi.ac.uk/pdbsum/1rkd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rkd RCSB]</span>
+== 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/1rkd_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=1rkd ConSurf].
+<div style="clear:both"></div>
-'''E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP'''
+==See Also==
+*[[Ribokinase 3D structures|Ribokinase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-BACKGROUND: D-ribose must be phosphorylated at O5' before it can be used in either anabolism or catabolism. This reaction is catalysed by ribokinase and requires the presence of ATP and magnesium. Ribokinase is a member of a family of carbohydrate kinases of previously unknown structure. RESULTS: The crystal structure of ribokinase from Escherichia coli in complex with ribose and dinucleotide was determined at 1.84 A resolution by multiple isomorphous replacement. There is one 33 kDa monomer of ribokinase in the asymmetric unit but the protein forms a dimer around a crystallographic twofold axis. Each subunit consists of a central alpha/beta unit, with a new type of nucleotide-binding fold, and a distinct beta sheet that forms a lid over the ribose-binding site. Contact between subunits involves orthogonal packing of beta sheets, in a novel dimer interaction that we call a beta clasp. CONCLUSIONS: Inspection of the complex indicates that ribokinase utilises both a catalytic base for activation of the ribose in nucleophilic attack and an anion hole that stabilises the transition state during phosphoryl transfer. The structure suggests an ordered reaction mechanism, similar to those proposed for other carbohydrate kinases that probably involves conformational changes. We propose that the beta-clasp structure acts as a lid, closing and opening upon binding and release of ribose. From these observations, an understanding of the structure and catalytic mechanism of related sugar kinases can be obtained.
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
-==About this Structure==
+[[Category: Cameron AD]]
-RKD 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=1RKD OCA].
+[[Category: Jones TA]]
+[[Category: Mowbray SL]]
-==Reference==
+[[Category: Sigrell JA]]
-Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures., Sigrell JA, Cameron AD, Jones TA, Mowbray SL, Structure. 1998 Feb 15;6(2):183-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9519409 9519409]
-[[Category: Escherichia coli]]
-[[Category: Ribokinase]]
-[[Category: Single protein]]
-[[Category: Cameron, A D.]]
-[[Category: Jones, T A.]]
-[[Category: Mowbray, S L.]]
-[[Category: Sigrell, J A.]]
-[[Category: carbohydrate kinase]]
-[[Category: nucleotide binding]]
-[[Category: ribose]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:29:22 2008''