1uwz: Difference between revisions

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-{{Seed}}
-[[Image:1uwz.png|left|200px]]
-<!--
+==Bacillus subtilis cytidine deaminase with an Arg56 - Ala substitution==
-The line below this paragraph, containing "STRUCTURE_1uwz", creates the "Structure Box" on the page.
+<StructureSection load='1uwz' size='340' side='right'caption='[[1uwz]], [[Resolution|resolution]] 1.99&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'>[[1uwz]] 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=1UWZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UWZ 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]] 1.99&#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_1uwz|  PDB=1uwz  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uwz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uwz OCA], [https://pdbe.org/1uwz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uwz RCSB], [https://www.ebi.ac.uk/pdbsum/1uwz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uwz 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/uw/1uwz_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=1uwz ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The zinc-containing cytidine deaminase (CDA, EC 3.5.4.5) is a pyrimidine salvage enzyme catalyzing the hydrolytic deamination of cytidine and 2'-deoxycytidine forming uridine and 2'-deoxyuridine, respectively. Homodimeric CDA (D-CDA) and homotetrameric CDA (T-CDA) both contain one zinc ion per subunit coordinated to the catalytic water molecule. The zinc ligands in D-CDA are one histidine and two cysteine residues, whereas in T-CDA zinc is coordinated to three cysteines. Two of the zinc coordinating cysteines in T-CDA form hydrogen bonds to the conserved residue Arg56, and this residue together with the dipole moments from two alpha-helices partially neutralizes the additional negative charge in the active site, leading to a catalytic activity similar to D-CDA. Arg56 has been substituted by a glutamine (R56Q), the corresponding residue in D-CDA, an alanine (R56A), and an aspartate (R56D). Moreover, one of the zinc-liganding cysteines has been substituted by histidine to mimic D-CDA, alone (C53H) and in combination with R56Q (C53H/R56Q). R56A, R56Q, and C53H/R56Q contain the same amount of zinc as the wild-type enzyme. The zinc-binding capacity of R56D is reduced. Only R56A, R56Q, and C53H/R56Q yielded measurable CDA activity, R56A and R56Q with similar K(m) but decreased V(max) values compared to wild-type enzyme. Because of dissociation into its inactive subunits, it was impossible to determine the kinetic parameters for C53H/R56Q. R56A and C53H/R56Q display increased apparent pK(a) values compared to the wild-type enzyme and R56Q. On the basis of the structures of R56A, R56Q, and C53H/R56Q an explanation is provided of kinetic results and the apparent instability of C53H/R56Q.
-===BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH AN ARG56- ALA SUBSTITUTION===
+Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase.,Johansson E, Neuhard J, Willemoes M, Larsen S Biochemistry. 2004 May 25;43(20):6020-9. PMID:15147186<ref>PMID:15147186</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1uwz" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15147186}}, adds the Publication Abstract to the page
+*[[Deaminase 3D structures|Deaminase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15147186 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15147186}}
+__TOC__
+</StructureSection>
-==About this Structure==
-UWZ 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=1UWZ OCA].
-==Reference==
-<ref group="xtra">PMID:15147186</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: Neuhard, J.]]
+[[Category: Neuhard J]]
-[[Category: Willemoes, M.]]
+[[Category: Willemoes M]]
-[[Category: Cdd]]
-[[Category: Cytidine deaminase]]
-[[Category: Hydrolase]]
-[[Category: Pyrimidine metabolism]]
-[[Category: Salvage]]
-[[Category: Tetramer]]
-[[Category: Zinc binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 10:09:26 2009''