1s2d: 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: @@
-{{Seed}}
-[[Image:1s2d.png|left|200px]]
-<!--
+==Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)==
-The line below this paragraph, containing "STRUCTURE_1s2d", creates the "Structure Box" on the page.
+<StructureSection load='1s2d' size='340' side='right'caption='[[1s2d]], [[Resolution|resolution]] 2.10&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'>[[1s2d]] 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=1S2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2D 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=V3M:(2~{S},3~{S},4~{R},5~{R})-3-fluoranyl-5-(hydroxymethyl)oxolane-2,4-diol'>V3M</scene></td></tr>
-{{STRUCTURE_1s2d|  PDB=1s2d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2d OCA], [https://pdbe.org/1s2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2d RCSB], [https://www.ebi.ac.uk/pdbsum/1s2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2d ProSAT]</span></td></tr>
+</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/s2/1s2d_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1s2d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)===
+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:14992575<ref>PMID:14992575</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_14992575}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1s2d" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 14992575 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14992575}}
+__TOC__
+</StructureSection>
-==About this Structure==
-S2D is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2D OCA].
-==Reference==
-<ref group="xtra">PMID:14992575</ref><references group="xtra"/>
 [[Category: Lactobacillus helveticus]]
-[[Category: Nucleoside deoxyribosyltransferase]]
+[[Category: Large Structures]]
-[[Category: Anand, R.]]
+[[Category: Anand R]]
-[[Category: Ealick, S E.]]
+[[Category: Ealick SE]]
-[[Category: Kaminski, P A.]]
+[[Category: Kaminski PA]]
-[[Category: Araa]]
-[[Category: Ptd]]
-[[Category: Ribosylate intermediate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 03:50:01 2009''