1k6w: Difference between revisions

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-[[Image:1k6w.jpg|left|200px]]<br /><applet load="1k6w" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1k6w, resolution 1.75&Aring;" />
-'''The Structure of Escherichia coli Cytosine Deaminase'''<br />
-==Overview==
+==The Structure of Escherichia coli Cytosine Deaminase==
-Cytosine deaminase (CD) catalyzes the deamination of cytosine, producing uracil. This enzyme is present in prokaryotes and fungi (but not multicellular eukaryotes) and is an important member of the pyrimidine salvage pathway in those organisms. The same enzyme also catalyzes the conversion of 5-fluorocytosine to 5-fluorouracil; this activity allows the formation of a cytotoxic chemotherapeutic agent from a non-cytotoxic precursor. The enzyme is of widespread interest both for antimicrobial drug design and for gene therapy applications against tumors. The structure of Escherichia coli CD has been determined in the presence and absence of a bound mechanism-based inhibitor. The enzyme forms an (alphabeta)(8) barrel structure with structural similarity to adenosine deaminase, a relationship that is undetectable at the sequence level, and no similarity to bacterial cytidine deaminase. The enzyme is packed into a hexameric assembly stabilized by a unique domain-swapping interaction between enzyme subunits. The active site is located in the mouth of the enzyme barrel and contains a bound iron ion that coordinates a hydroxyl nucleophile. Substrate binding involves a significant conformational change that sequesters the reaction complex from solvent.
+<StructureSection load='1k6w' size='340' side='right'caption='[[1k6w]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1k6w]] 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=1K6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K6W FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1k6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k6w OCA], [https://pdbe.org/1k6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k6w RCSB], [https://www.ebi.ac.uk/pdbsum/1k6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k6w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CODA_ECOLI CODA_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/k6/1k6w_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=1k6w ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-K6W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=FE:'>FE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cytosine_deaminase Cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.1 3.5.4.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K6W OCA].
+*[[Deaminase 3D structures|Deaminase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-The structure of Escherichia coli cytosine deaminase., Ireton GC, McDermott G, Black ME, Stoddard BL, J Mol Biol. 2002 Jan 25;315(4):687-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11812140 11812140]
-[[Category: Cytosine deaminase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Black, M E.]]
+[[Category: Black ME]]
-[[Category: Ireton, G C.]]
+[[Category: Ireton GC]]
-[[Category: McDermott, G.]]
+[[Category: McDermott G]]
-[[Category: Stoddard, B L.]]
+[[Category: Stoddard BL]]
-[[Category: FE]]
-[[Category: alpha-beta barrel]]
-[[Category: cytosine deaminase]]
-[[Category: domain swap]]
-[[Category: hexamer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:30:48 2008''