1s2g: Difference between revisions

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-[[Image:1s2g.jpg|left|200px]]<br /><applet load="1s2g" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1s2g, resolution 2.10&Aring;" />
-'''Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine'''<br />
-==Overview==
+==Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine==
-The structure of class I N-deoxyribosyltransferase from Lactobacillus, helveticus was determined by X-ray crystallography. Unlike class II, N-deoxyribosyltransferases, which accept either purine or pyrimidine, deoxynucleosides, class I enzymes are specific for purines as both the, donor and acceptor base. Both class I and class II enzymes are highly, specific for deoxynucleosides. The class I structure reveals similarities, with the previously determined class II enzyme from Lactobacillus, leichmanni [Armstrong, S. A., Cook, W. J., Short, S. A., and Ealick, S. E., (1996) Structure 4, 97-107]. The specificity of the class I enzyme for, purine deoxynucleosides can be traced to a loop (residues 48-62), which, shields the active site in the class II enzyme. In the class I enzyme, the, purine base itself shields the active site from the solvent, while the, smaller pyrimidine base cannot. The structure of the enzyme with a bound, ribonucleoside shows that the nucleophilic oxygen atom of Glu101 hydrogen, bonds to the O2' atom, rendering it unreactive and thus explaining the, specificity for 2'-deoxynucleosides. The structure of a ribosylated enzyme, intermediate reveals movements that occur during cleavage of the, N-glycosidic bond. The structures of complexes with substrates and, substrate analogues show that the purine base can bind in several, different orientations, thus explaining the ability of the enzyme to, catalyze alternate deoxyribosylation at the N3 or N7 position.
+<StructureSection load='1s2g' size='340' side='right'caption='[[1s2g]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1s2g]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2G FirstGlance]. <br>
-S2G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus] with 3D1 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S2G OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2g OCA], [https://pdbe.org/1s2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2g RCSB], [https://www.ebi.ac.uk/pdbsum/1s2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2g ProSAT]</span></td></tr>
-Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution., Anand R, Kaminski PA, Ealick SE, Biochemistry. 2004 Mar 9;43(9):2384-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14992575 14992575]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8RLY5_LACHE Q8RLY5_LACHE]
+== 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/s2/1s2g_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=1s2g ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Lactobacillus helveticus]]
-[[Category: Nucleoside deoxyribosyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Anand R]]
-[[Category: Anand, R.]]
+[[Category: Ealick SE]]
-[[Category: Ealick, S.E.]]
+[[Category: Kaminski PA]]
-[[Category: Kaminski, P.A.]]
-[[Category: 3D1]]
-[[Category: 2'-deoxyadenosine]]
-[[Category: 2'-purine deoxyribosyltansferase]]
-[[Category: ptd]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:45:34 2007''