3lg1
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3lg1 is ON HOLD Authors: Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Filimonenkov, A.A., Dorovatovsky, P.V., Tikhonova, T.V., Popov, V.O. Descript...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium borohydride (in complex with sulfite)== | |
| + | <StructureSection load='3lg1' size='340' side='right'caption='[[3lg1]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3lg1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thioalkalivibrio_nitratireducens Thioalkalivibrio nitratireducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LG1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LG1 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</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=3lg1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lg1 OCA], [https://pdbe.org/3lg1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lg1 RCSB], [https://www.ebi.ac.uk/pdbsum/3lg1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lg1 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/NIR_THIND NIR_THIND] Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process (PubMed:16500161, PubMed:22281743). Has very low activity toward hydroxylamine (PubMed:16500161). Has even lower activity toward sulfite (PubMed:16500161, PubMed:22281743). Sulfite reductase activity is maximal at neutral pH (PubMed:20944237).<ref>PMID:16500161</ref> <ref>PMID:20944237</ref> <ref>PMID:22281743</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg residues. The distinguishing structural feature of TvNiR is the presence of a covalent bond between the CE2 atom of the catalytic Tyr303 and the S atom of Cys305, which might be responsible for the higher nitrite reductase activity of TvNiR compared with NrfAs. In the present study, a new modified form of the enzyme (TvNiRb) that contains an additional covalent bond between Tyr303 CE1 and Gln360 CG is reported. Structures of TvNiRb in complexes with phosphate (1.45 A resolution) and sulfite (1.8 A resolution), the structure of TvNiR in a complex with nitrite (1.83 A resolution) and several additional structures were determined. The formation of the second covalent bond by Tyr303 leads to a decrease in both the nitrite and sulfite reductase activities of the enzyme. Tyr303 is located at the exit from the putative proton-transport channel to the active site, which is absent in NrfAs. This is an additional argument in favour of the involvement of Tyr303 as a proton donor in catalysis. The changes in the activity of cytochrome c nitrite reductases owing to the formation of Tyr-Cys and Tyr-Gln bonds may be associated with changes in the pK(a) value of the catalytic tyrosine. | ||
| - | + | Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity.,Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovskii PV, Popov VO Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):144-53. Epub 2012, Jan 13. PMID:22281743<ref>PMID:22281743</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3lg1" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| + | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thioalkalivibrio nitratireducens]] | ||
| + | [[Category: Boyko KM]] | ||
| + | [[Category: Dorovatovsky PV]] | ||
| + | [[Category: Filimonenkov AA]] | ||
| + | [[Category: Polyakov KM]] | ||
| + | [[Category: Popov VO]] | ||
| + | [[Category: Tikhonova TV]] | ||
| + | [[Category: Trofimov AA]] | ||
Current revision
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium borohydride (in complex with sulfite)
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