1sz3: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEXED WITH GNP AND MG+2==
-<StructureSection load='1sz3' size='340' side='right' caption='[[1sz3]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='1sz3' size='340' side='right'caption='[[1sz3]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sz3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sz3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SZ3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR1025 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sz3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sz3 RCSB], [http://www.ebi.ac.uk/pdbsum/1sz3 PDBsum], [http://www.topsan.org/Proteins/BSGC/1sz3 TOPSAN]</span></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=1sz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sz3 OCA], [https://pdbe.org/1sz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sz3 RCSB], [https://www.ebi.ac.uk/pdbsum/1sz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sz3 ProSAT], [https://www.topsan.org/Proteins/BSGC/1sz3 TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Y1025_DEIRA Y1025_DEIRA] Hydrolase that can act as a nucleoside triphosphatase and a dinucleoside polyphosphate pyrophosphatase. The best substrates are 8-oxo-dGTP and 8-oxo-GTP. Other substrates include Ap4A, dGTP and GTP. May be involved in protection from damage caused by radiation.<ref>PMID:23481913</ref>
 == 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/sz/1sz3_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sz/1sz3_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1sz3 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-We have determined the crystal structure, at 1.4A, of the Nudix hydrolase DR1025 from the extremely radiation resistant bacterium Deinococcus radiodurans. The protein forms an intertwined homodimer by exchanging N-terminal segments between chains. We have identified additional conserved elements of the Nudix fold, including the metal-binding motif, a kinked beta-strand characterized by a proline two positions upstream of the Nudix consensus sequence, and participation of the N-terminal extension in the formation of the substrate-binding pocket. Crystal structures were also solved of DR1025 crystallized in the presence of magnesium and either a GTP analog or Ap(4)A (both at 1.6A resolution). In the Ap(4)A co-crystal, the electron density indicated that the product of asymmetric hydrolysis, ATP, was bound to the enzyme. The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved.
-Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes.,Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu W, Bessman MJ, Brenner SE, Holbrook SR J Mol Biol. 2004 May 21;339(1):103-16. PMID:15123424<ref>PMID:15123424</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
+*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
 == References ==
 <references/>
@@ Line 30: / Line 29: @@
 </StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Structural genomic]]
+[[Category: Large Structures]]
-[[Category: Bessman, M J]]
+[[Category: Bessman MJ]]
-[[Category: Brenner, S E]]
+[[Category: Brenner SE]]
-[[Category: Hill, E E]]
+[[Category: Hill EE]]
-[[Category: Holbrook, E L]]
+[[Category: Holbrook EL]]
-[[Category: Holbrook, S R]]
+[[Category: Holbrook SR]]
-[[Category: Mooster, J L]]
+[[Category: Mooster JL]]
-[[Category: Ranatunga, W]]
+[[Category: Ranatunga W]]
-[[Category: Schulze-Gahmen, U]]
+[[Category: Schulze-Gahmen U]]
-[[Category: Xu, W]]
+[[Category: Xu W]]
-[[Category: Alpha-beta-alpha sandwich]]
-[[Category: Bsgc structure funded by nih]]
-[[Category: Hydrolase]]
-[[Category: Nudix fold]]
-[[Category: PSI, Protein structure initiative]]