3rkh

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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[3rkh]] 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=3RKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKH FirstGlance]. <br>
-</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=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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]] 1.83&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ot4|2ot4]], [[3f29|3f29]]</div></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=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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=3rkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkh OCA], [https://pdbe.org/3rkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rkh RCSB], [https://www.ebi.ac.uk/pdbsum/3rkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/Q5F2I3_9GAMM Q5F2I3_9GAMM]] Plays a role in nitrite reduction (By similarity).[SAAS:SAAS003321_004_001592]
+[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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3rkh" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 28: / Line 19: @@
 [[Category: Large Structures]]
 [[Category: Thioalkalivibrio nitratireducens]]
-[[Category: Dorovatovskii, P V]]
+[[Category: Dorovatovskii PV]]
-[[Category: Polyakov, K M]]
+[[Category: Polyakov KM]]
-[[Category: Popov, V O]]
+[[Category: Popov VO]]
-[[Category: Tikhonov, A V]]
+[[Category: Tikhonov AV]]
-[[Category: Tikhonova, T V]]
+[[Category: Tikhonova TV]]
-[[Category: Trofimov, A A]]
+[[Category: Trofimov AA]]
-[[Category: Eight hemes c]]
-[[Category: Nitrite reductase]]
-[[Category: Oxidoreductase]]
-[[Category: Tyr-cys covalent bond]]

3rkh

From Proteopedia

Current revision

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

Structural highlights

Function

See Also

References

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