4l3y: Difference between revisions

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==Nitrite complex of TvNiR, high dose data set (NO complex)==
==Nitrite complex of TvNiR, high dose data set (NO complex)==
<StructureSection load='4l3y' size='340' side='right' caption='[[4l3y]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='4l3y' size='340' side='right'caption='[[4l3y]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4l3y]] 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=4L3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L3Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[4l3y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thioalkalivibrio_nitratireducens_DSM_14787 Thioalkalivibrio nitratireducens DSM 14787]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L3Y 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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]] 1.95&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4l38|4l38]], [[4l3x|4l3x]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </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=4l3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l3y OCA], [https://pdbe.org/4l3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l3y RCSB], [https://www.ebi.ac.uk/pdbsum/4l3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l3y ProSAT]</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=4l3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l3y OCA], [http://pdbe.org/4l3y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l3y RCSB], [http://www.ebi.ac.uk/pdbsum/4l3y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l3y ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/L0DSL2_THIND L0DSL2_THIND]] 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>
 
==See Also==
*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thioalkalivibrio nitratireducens]]
[[Category: Large Structures]]
[[Category: Lazarenko, V A]]
[[Category: Thioalkalivibrio nitratireducens DSM 14787]]
[[Category: Polyakov, K M]]
[[Category: Lazarenko VA]]
[[Category: Popov, A N]]
[[Category: Polyakov KM]]
[[Category: Popov, V O]]
[[Category: Popov AN]]
[[Category: Tikhonov, A V]]
[[Category: Popov VO]]
[[Category: Tikhonova, T V]]
[[Category: Tikhonov AV]]
[[Category: Trofimov, A A]]
[[Category: Tikhonova TV]]
[[Category: Hemes c]]
[[Category: Trofimov AA]]
[[Category: Oxidoreductase]]

Latest revision as of 17:28, 29 November 2023

Nitrite complex of TvNiR, high dose data set (NO complex)Nitrite complex of TvNiR, high dose data set (NO complex)

Structural highlights

4l3y is a 2 chain structure with sequence from Thioalkalivibrio nitratireducens DSM 14787. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
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]

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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

4l3y, resolution 1.95Å

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