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3sce

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Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)

Structural highlights

3sce is a 2 chain structure with sequence from Thioalkalivibrio nitratireducens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.45Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3]

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tikhonova TV, Slutsky A, Antipov AN, Boyko KM, Polyakov KM, Sorokin DY, Zvyagilskaya RA, Popov VO. Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. Biochim Biophys Acta. 2006 Apr;1764(4):715-23. Epub 2006 Feb 9. PMID:16500161 doi:http://dx.doi.org/10.1016/j.bbapap.2005.12.021
↑ Trofimov AA, Polyakov KM, Boyko KM, Tikhonova TV, Safonova TN, Tikhonov AV, Popov AN, Popov VO. Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide. Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1043-7. Epub 2010, Sep 18. PMID:20944237 doi:10.1107/S0907444910031665
↑ Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovskii PV, Popov VO. Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):144-53. Epub 2012, Jan 13. PMID:22281743 doi:10.1107/S0907444911052632
↑ Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovskii PV, Popov VO. Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):144-53. Epub 2012, Jan 13. PMID:22281743 doi:10.1107/S0907444911052632

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3sce"

@@ Line 1: / Line 1: @@
 ==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)==
-<StructureSection load='3sce' size='340' side='right' caption='[[3sce]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+<StructureSection load='3sce' size='340' side='right'caption='[[3sce]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3sce]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thioalkalivibrio_nitratireducens Thioalkalivibrio nitratireducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SCE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SCE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3sce]] 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=3SCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SCE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=PO4:PHOSPHATE+ION'>PO4</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]] 1.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ot4|2ot4]]</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=PO4:PHOSPHATE+ION'>PO4</scene></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=3sce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sce OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sce RCSB], [http://www.ebi.ac.uk/pdbsum/3sce PDBsum]</span></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=3sce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sce OCA], [https://pdbe.org/3sce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sce RCSB], [https://www.ebi.ac.uk/pdbsum/3sce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sce 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 ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3sce" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nitric reductase|Nitric reductase]]
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thioalkalivibrio nitratireducens]]
-[[Category: Boyko, K M]]
+[[Category: Boyko KM]]
-[[Category: Polyakov, K M]]
+[[Category: Polyakov KM]]
-[[Category: Popov, V O]]
+[[Category: Popov VO]]
-[[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-gln and tyr-cys bond]]

3sce

From Proteopedia

Current revision

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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