7pd1
From Proteopedia
(Difference between revisions)
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==Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase ThiH (2-iminoacetate synthase) from Thermosinus carboxydivorans== | ==Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase ThiH (2-iminoacetate synthase) from Thermosinus carboxydivorans== | ||
| - | <StructureSection load='7pd1' size='340' side='right'caption='[[7pd1]]' scene=''> | + | <StructureSection load='7pd1' size='340' side='right'caption='[[7pd1]], [[Resolution|resolution]] 1.27Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7pd1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosinus_carboxydivorans_Nor1 Thermosinus carboxydivorans Nor1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD1 FirstGlance]. <br> |
| - | </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=7pd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd1 OCA], [https://pdbe.org/7pd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd1 ProSAT]</span></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]] 1.27Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></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=7pd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd1 OCA], [https://pdbe.org/7pd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd1 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A1HPQ5_9FIRM A1HPQ5_9FIRM] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 2-iminoacetate synthase ThiH is a radical S-adenosyl-L-methionine (SAM) L-tyrosine lyase and catalyzes the L-tyrosine Calpha-Cbeta bond break to produce dehydroglycine and p-cresol while the radical SAM L-tryptophan lyase NosL cleaves the L-tryptophan Calpha-C bond to produce 3-methylindole-2-carboxylic acid. It has been difficult to understand the features that condition one C-C bond break over the other one because the two enzymes display significant primary structure similarities and presumably similar substrate-binding modes. Here, we report the crystal structure of L-tyrosine bound ThiH from Thermosinus carboxydivorans revealing an unusual protonation state of L-tyrosine upon binding. Structural comparison of ThiH with NosL and computational studies of the respective reactions they catalyze show that substrate activation is eased by tunneling effect and that subtle structural changes between the two enzymes affect, in particular, the hydrogen-atom abstraction by the 5 -deoxyadenosyl radical species, driving the difference in reaction specificity. | ||
| + | |||
| + | L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases.,Amara P, Saragaglia C, Mouesca JM, Martin L, Nicolet Y Nat Commun. 2022 Apr 27;13(1):2284. doi: 10.1038/s41467-022-29980-4. PMID:35477710<ref>PMID:35477710</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7pd1" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Thermosinus carboxydivorans Nor1]] | ||
[[Category: Amara P]] | [[Category: Amara P]] | ||
[[Category: Martin L]] | [[Category: Martin L]] | ||
Current revision
Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase ThiH (2-iminoacetate synthase) from Thermosinus carboxydivorans
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