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4k9r

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Spore photoproduct lyase Y98F mutant

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Retrieved from "http://52.214.119.220/wiki/index.php/4k9r"

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 ==Spore photoproduct lyase Y98F mutant==
-<StructureSection load='4k9r' size='340' side='right' caption='[[4k9r]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='4k9r' size='340' side='right'caption='[[4k9r]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4k9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geotn Geotn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K9R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4k9r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K9R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fhc|4fhc]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GTNG_2348 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=420246 GEOTN])</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=4k9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k9r OCA], [https://pdbe.org/4k9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k9r RCSB], [https://www.ebi.ac.uk/pdbsum/4k9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k9r 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/Spore_photoproduct_lyase Spore photoproduct lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.14 4.1.99.14] </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=4k9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k9r OCA], [http://pdbe.org/4k9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k9r RCSB], [http://www.ebi.ac.uk/pdbsum/4k9r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k9r ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A4IQU1_GEOTN A4IQU1_GEOTN]
-Spore photoproduct lyase (SPL) repairs a covalent UV-induced thymine dimer, spore photoproduct (SP), in germinating endospores and is responsible for the strong UV resistance of endospores. SPL is a radical S-adenosyl-l-methionine (SAM) enzyme, which uses a [4Fe-4S](+) cluster to reduce SAM, generating a catalytic 5'-deoxyadenosyl radical (5'-dA(*)). This in turn abstracts a H atom from SP, generating an SP radical that undergoes beta scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. Recent biochemical and structural data suggest that a conserved cysteine donates a H atom to the thymine radical, resulting in a putative thiyl radical. Here we present structural and biochemical data that suggest that two conserved tyrosines are also critical in enzyme catalysis. One [Y99(Bs) in Bacillus subtilis SPL] is downstream of the cysteine, suggesting that SPL uses a novel hydrogen atom transfer (HAT) pathway with a pair of cysteine and tyrosine residues to regenerate SAM. The other tyrosine [Y97(Bs)] has a structural role to facilitate SAM binding; it may also contribute to the SAM regeneration process by interacting with the putative (*)Y99(Bs) and/or 5'-dA(*) intermediates to lower the energy barrier for the second H abstraction step. Our results indicate that SPL is the first member of the radical SAM superfamily (comprising more than 44000 members) to bear a catalytically operating HAT chain.
-A radical transfer pathway in spore photoproduct lyase.,Yang L, Nelson RS, Benjdia A, Lin G, Telser J, Stoll S, Schlichting I, Li L Biochemistry. 2013 May 7;52(18):3041-50. doi: 10.1021/bi3016247. Epub 2013 Apr, 22. PMID:23607538<ref>PMID:23607538</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4k9r" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Geotn]]
+[[Category: Geobacillus thermodenitrificans NG80-2]]
-[[Category: Spore photoproduct lyase]]
+[[Category: Large Structures]]
-[[Category: Benjdia, A]]
+[[Category: Benjdia A]]
-[[Category: Li, L]]
+[[Category: Li L]]
-[[Category: Lin, G]]
+[[Category: Lin G]]
-[[Category: Nelson, R S]]
+[[Category: Nelson RS]]
-[[Category: Schlichting, I]]
+[[Category: Schlichting I]]
-[[Category: Stoll, S]]
+[[Category: Stoll S]]
-[[Category: Telser, J]]
+[[Category: Telser J]]
-[[Category: Yang, L]]
+[[Category: Yang L]]
-[[Category: Dna repair]]
-[[Category: Lyase]]
-[[Category: Partial tim barrel]]

4k9r

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Spore photoproduct lyase Y98F mutant

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