1jtk: Difference between revisions

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-{{Seed}}
-[[Image:1jtk.png|left|200px]]
-<!--
+==Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine==
-The line below this paragraph, containing "STRUCTURE_1jtk", creates the "Structure Box" on the page.
+<StructureSection load='1jtk' size='340' side='right'caption='[[1jtk]], [[Resolution|resolution]] 2.04&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'>[[1jtk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JTK 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]] 2.04&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THU:TETRAHYDRODEOXYURIDINE'>THU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1jtk|  PDB=1jtk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jtk OCA], [https://pdbe.org/1jtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jtk RCSB], [https://www.ebi.ac.uk/pdbsum/1jtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jtk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDD_BACSU CDD_BACSU] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
+== 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/jt/1jtk_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=1jtk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cytidine deaminases (CDA, EC 3.5.4.5) are zinc-containing enzymes in the pyrimidine salvage pathway that catalyze the formation of uridine and deoxyuridine from cytidine and deoxycytidine, respectively. Two different classes have been identified in the CDA family, a homodimeric form (D-CDA) with two zinc ions per dimer and a homotetrameric form (T-CDA) with four zinc ions per tetramer. We have determined the first structure of a T-CDA from Bacillus subtilis. The active form of T-CDA is assembled of four identical subunits with one active site apiece. The subunit of D-CDA is composed of two domains each exhibiting the same fold as the T-CDA subunits, but only one of them contains zinc in the active site. The similarity results in a conserved structural core in the two CDA forms. An intriguing difference between the two CDA structures is the zinc coordinating residues found at the N-terminal of two alpha-helices: three cysteine residues in the tetrameric form and two cysteine residues and one histidine residue in the dimeric form. The role of the zinc ion is to activate a water molecule and thereby generate a hydroxide ion. How the zinc ion in T-CDA surrounded with three negatively charged residues can create a similar activity of T-CDA compared to D-CDA has been an enigma. However, the structure of T-CDA reveals that the negative charge caused by the three ligands is partly neutralized by (1) an arginine residue hydrogen-bonded to two of the cysteine residues and (2) the dipoles of two alpha-helices.
-===Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine===
+Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.,Johansson E, Mejlhede N, Neuhard J, Larsen S Biochemistry. 2002 Feb 26;41(8):2563-70. PMID:11851403<ref>PMID:11851403</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1jtk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11851403}}, adds the Publication Abstract to the page
+*[[Deaminase 3D structures|Deaminase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11851403 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11851403}}
+__TOC__
+</StructureSection>
-==About this Structure==
-JTK is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA].
-==Reference==
-<ref group="xtra">PMID:11851403</ref><references group="xtra"/>
 [[Category: Bacillus subtilis]]
-[[Category: Cytidine deaminase]]
+[[Category: Large Structures]]
-[[Category: Johansson, E.]]
+[[Category: Johansson E]]
-[[Category: Larsen, S.]]
+[[Category: Larsen S]]
-[[Category: Mejlhede, N.]]
+[[Category: Mejlhede N]]
-[[Category: Neuhard, J.]]
+[[Category: Neuhard J]]
-[[Category: Cda]]
-[[Category: Cytidine deaminase]]
-[[Category: Pyrimidine salvage pathway]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:02:40 2009''