3lgs: Difference between revisions

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 ==A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine==
-<StructureSection load='3lgs' size='340' side='right' caption='[[3lgs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3lgs' size='340' side='right'caption='[[3lgs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lgs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LGS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lgs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LGS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jys|1jys]], [[1nc1|1nc1]], [[2qtt|2qtt]], [[2qtg|2qtg]], [[2qsu|2qsu]], [[2h8g|2h8g]], [[1nc3|1nc3]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT4g38800, atmtan1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=3lgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgs OCA], [https://pdbe.org/3lgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lgs RCSB], [https://www.ebi.ac.uk/pdbsum/3lgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgs ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylthioadenosine_nucleosidase Methylthioadenosine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.16 3.2.2.16] </span></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=3lgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgs OCA], [http://pdbe.org/3lgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lgs RCSB], [http://www.ebi.ac.uk/pdbsum/3lgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgs ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MTN1_ARATH MTN1_ARATH]] Enzyme of the methionine cycle that catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis. Inactive towards S-adenosylhomocysteine (SAH/AdoHcy).<ref>PMID:17144895</ref> <ref>PMID:18342331</ref> <ref>PMID:20345605</ref>
+[https://www.uniprot.org/uniprot/MTN1_ARATH MTN1_ARATH] Enzyme of the methionine cycle that catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis. Inactive towards S-adenosylhomocysteine (SAH/AdoHcy).<ref>PMID:17144895</ref> <ref>PMID:18342331</ref> <ref>PMID:20345605</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=3lgs ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2A resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.
-Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.,Siu KK, Asmus K, Zhang AN, Horvatin C, Li S, Liu T, Moffatt B, Woods VL Jr, Howell PL J Struct Biol. 2010 Jun 8. PMID:20554051<ref>PMID:20554051</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3lgs" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Methylthioadenosine nucleosidase]]
+[[Category: Large Structures]]
-[[Category: Howell, P L]]
+[[Category: Howell PL]]
-[[Category: Siu, K K.W]]
+[[Category: Siu KKW]]
-[[Category: Hydrolase]]