Cytochrome c nitrite reductase

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== Structural highlights ==
== Structural highlights ==
-
Cytochrome c nitrite reductase with <scene name='83/833267/Cv/5'>5 heme groups</scene> (PDB code [[2e80]]). In the ''Wolinella succinogenes'' ccNiR structure the <scene name='83/833267/Cv/2'>substrate NO2 binds to the Fe+3 atom of the heme group and makes hydrogen bonds to side chains of residues R114 and H277</scene><ref>PMID:12296741</ref>. <scene name='83/833267/Cv/4'>NO2 hydrogen bonds via water molecules</scene>. Water molecules are shown as red spheres. Rare-earth element <scene name='83/833267/Cv/6'>Yttrium ion binding site</scene>.
+
Cytochrome c nitrite reductase with <scene name='83/833267/Cv/5'>5 heme groups</scene> (PDB code [[2e80]]). In the ''Wolinella succinogenes'' ccNiR structure the <scene name='83/833267/Cv/2'>substrate NO2 binds to the Fe+3 atom of the heme group and makes hydrogen bonds to side chains of residues R114 and H277</scene><ref>PMID:12296741</ref>. <scene name='83/833267/Cv/4'>NO2 hydrogen bonds via water molecules also with other residues</scene>. Water molecules are shown as red spheres. Rare-earth element <scene name='83/833267/Cv/6'>Yttrium ion binding site</scene>.
</StructureSection>
</StructureSection>
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**[[1fs7]], [[1fs8]], [[1fs9]], ]]3bnf]] – WsccNiR – ''Wolinella succinogenes''<br />
**[[1fs7]], [[1fs8]], [[1fs9]], ]]3bnf]] – WsccNiR – ''Wolinella succinogenes''<br />
**[[3bng]], [[3bnj]] – WsccNiR (mutant)<br />
**[[3bng]], [[3bnj]] – WsccNiR (mutant)<br />
-
**[[1gu6]], [[2rdz]], [[3l1t]], [[3tor]] – EcccNiR – ''Eschericia coli''<br />
+
**[[1gu6]], [[2rdz]], [[3l1t]], [[3tor]] – EcccNiR – ''Eschericia coli<''br />
**[[2rf7]], [[4wjy]] – EcccNiR (mutant)<br />
**[[2rf7]], [[4wjy]] – EcccNiR (mutant)<br />
-
**[[2zo5]], [[3f29]], [[3gm6]], [[3mmo]], [[3ttb]], [[3uu9]], [[3fo3]], [[3lg1]], [[3lgq]] – TnccNiR – ''Thioalkalivibrio nitratireducens''<br />
+
**[[6p73]], [[9cuf]] – SoccNiR – ''Shewanella oneidensis'' <br />
-
**[[3sce]], [[2ot4]], [[4l3x]], [[4l3y]], [[4l3z]], [[4q0t]], [[4q17]], [[4q1o]], [[4q4u]], [[4q5b]], [[4q5c]] – TnccNiR 8 hemes<br />
+
**[[3ubr]] – SoccNiR - Laue<br />
-
**[[3ubr]] – ccNiR – ''Shewanella oneidensis'' - Laue<br />
+
**[[2j7a]] – DvccNiR – ''Desulfovibrio vulgaris''<br />
**[[2j7a]] – DvccNiR – ''Desulfovibrio vulgaris''<br />
**[[1oah]] – ccNiR – ''Desulfovibrio desulfuricans''<br />
**[[1oah]] – ccNiR – ''Desulfovibrio desulfuricans''<br />
 +
**[[6v0a]] – ccNiR – ''Geobacter lovleyi''<br />
*Cytochrome c nitrite reductase complex
*Cytochrome c nitrite reductase complex
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**[[3bnh]] – WsccNiR (mutant) + NO2<br />
**[[3bnh]] – WsccNiR (mutant) + NO2<br />
**[[2e81]] – WsccNiR + hydroxylamine<br />
**[[2e81]] – WsccNiR + hydroxylamine<br />
 +
**[[2vr0]] – DvccNiR catalytic subunit + NRFH + quinolone derivative<br />
 +
 +
*Eight-heme nitrite reductase
 +
 +
**[[2ot4]], [[2zo5]], [[3f29]], [[3gm6]], [[3mmo]], [[3ttb]], [[3uu9]], [[3fo3]], [[3lg1]], [[3lgq]], [[3sce]], [[4l3x]], [[4l3y]], [[4l3z]], [[4q0t]], [[4q17]], [[4q1o]], [[4q4u]], [[4q5b]], [[4q5c]] – TnccNiR – ''Thioalkalivibrio nitratireducens''<br />
 +
**[[7o9u]] – TnccNiR – NMR<br />
**[[3owm]], [[3s7w]] – TnccNiR + hydroxylamine<br />
**[[3owm]], [[3s7w]] – TnccNiR + hydroxylamine<br />
**[[3d1i]], [[3rkh]] – TnccNiR + NO2<br />
**[[3d1i]], [[3rkh]] – TnccNiR + NO2<br />
-
**[[2vr0]] – DvccNiR catalytic subunit + NRFH + quinolone derivative<br />
+
**[[8rv0]] – ccNiR + NO2 + NO – ''Trichlorobacter ammonificans''<br />
 +
 
 +
*'''Heme-containing nitrite reductase - (Cytochrome C-552)'''
 +
 
 +
**[[1aof]], [[1qks]], [[1hj4]], [[1hj5]], [[1h9x]], [[1hcm]] - PpNIR – ''Paracoccus pantotrophus''<br />
 +
**[[1gq1]] - PpNIR (mutant)<br />
 +
**[[1nir]], [[1bl9]], [[1n15]], [[1n50]], [[1n90]], [[6rtd]], [[6rte]], [[6tpo]], [[6tsi]] – PaNIR – ''Pseudomonas aeruginosa''<br />
 +
**[[1hzu]] - PaNIR (mutant)<br />
 +
**[[1qdb]] - NIR – ''Sulfurospirillum deleyianum''<br />
 +
**[[1fs7]], [[1fs8]] - WsNIR – ''Wolinella succinogenes''<br />
 +
**[[3bng]] - WsNIR (mutant) <br />
 +
**[[1gu6]], [[2rdz]], [[3tor]] – EcNIR – ''Escherichia coli''<br />
 +
**[[2rf7]], [[4wjy]] - EcNIR (mutant) <br />
 +
**[[2jo6]] – EcNIR small subunit – NMR<BR />
 +
**[[2jza]] - NIR small subunit – ''Pectobacterium atrosepticum'' - NMR<BR />
 +
**[[1oah]] – NIR – ''Desulfovibrio desulfuricans''<br />
 +
**[[2j7a]] - DvNIR – ''Desulfovibrio vulgaris''<br />
 +
**[[2ot4]], [[3gm6]], [[3fo3]], [[3sce]], [[3uu9]], [[4q0t]], [[4q17]], [[4q1o]], [[4q4u]], [[4q5b]], [[4q5c]] - TnNIR – ''Thioalkalivibrio nitratireducens''<br />
 +
**[[3m97]] – PdNIR soluble domain – ''Paracoccus denitrificans''<br />
 +
**[[2ai5]] – HtNIR – ''Hydrogenophilus thermophilus'' – NMR<BR />
 +
**[[2d0s]], [[1ynr]], [[3vym]] – HtNIR<BR />
 +
**[[1ayg]] – NIR - ''Hydrogenobacter thermoluteolus'' – NMR<BR />
 +
**[[1i6d]], [[1i6e]], [[1c7m]] – PdNIR functional domain – NMR<BR />
 +
**[[1ql3]], [[1ql4]] - PdNIR functional domain<BR />
 +
**[[1dt1]], [[1qyz]], [[1r0q]], [[1c52]], [[3vnw]] – TtNIR – ''Thermus thermophilus''<BR />
 +
**[[2fwl]] – TtNIR + NIR oxidase subunit II <BR />
 +
**[[1cno]] – NIR – ''Pseudomonas nautica''<br />
 +
**[[3ubr]], [[6p73]] – SoNIR – ''Shewanella oneidensis''<br />
 +
**[[3sqx]] – TpNIR – ''Thioalkalivibrio paradoxus''<br />
 +
**[[6v0a]] – NIR – ''Geobacter lovleyi''<br />
 +
 
 +
*Heme-containing nitrite reductase binary complex
 +
 
 +
**[[1dy7]] - PpNIR + CO<br />
 +
**[[1hj3]] - PpNIR + O2<br />
 +
**[[2e81]] - WsNIR + NH2OH<br />
 +
**[[3bnf]] - WsNIR + sulfite <BR />
 +
**[[2vr0]] - DvNIR + HQNO inhibitor<br />
 +
**[[3ziy]], [[4ax3]], [[6fja]], [[6f1q]] – RpNIR + Cu – ''Ralstonia pickettii''<br />
 +
**[[3ayf]] – NIR + Zn – ''Geobacillus stearothermophilus''<br />
 +
**[[2yqb]], [[3zbm]] – RpNIR (mutant) + Cu <br />
 +
**[[3o0r]] – PaNIR + antibody<br />
 +
**[[5guw]] – PaNIR + nitric oxide reductase<br />
 +
**[[3sxq]] – TpNIR + Co<br />
 +
 
 +
*Heme-containing nitrite reductase binary complex with cyanide
 +
 
 +
**[[1h9y]] - PpNIR + CN<br />
 +
**[[1gjq]] - PaNIR + CN<br />
 +
**[[1e2r]] - PdNIR+ CN <br />
 +
 
 +
*Heme-containing nitrite reductase binary complex with nitric oxide
 +
 
 +
**[[1nno]] - PaNIR + NO<br />
 +
**[[1hzv]] - PaNIR (mutant) + NO<br />
 +
**[[1aom]], [[1aoq]], [[5ocb]], [[5ocf]] - PpNIR + NO + NO2<br />
 +
** [[5obo]] - PpNIR (mutant) + Cu + NO2<br />
 +
 
 +
*Heme-containing nitrite reductase binary complex with nitrite
 +
 
 +
**[[2e80]] - WsNIR + NO2<br />
 +
**[[3bnh]] - WsNIR (mutant) + NO<br />
 +
**[[3d1i]], [[3rkh]], [[3owm]], [[4l38]], [[4l3x]], [[4l3y]], [[4l3z]] - TnNIR + NO2<br />
 +
** [[6qwg]] - AcNIR + Cu + NO2<br />
 +
** [[6tfd]] - HdNIR + Cu + NO2<br />
 +
 
 +
*Heme-containing nitrite reductase binary complex with azide
 +
 
 +
**[[2zo5]] - TnNIR + N3<br />
 +
**[[3s7w]] - TnNIR + NO2 + N3<br />
 +
**[[1fs9]] - WsNIR + N3
 +
 
 +
*Heme-containing nitrite reductase binary complex with sulfite
 +
 
 +
**[[3mmo]] - WsNIR + SO3<BR />
 +
**[[3bnj]] - WsNIR (mutant) + SO3<BR />
 +
**[[3lg1]], [[3lgq]], [[3f29]], [[3ttb]] - TnNIR + SO3<BR />
 +
**[[3l1t]] - EcNIR + SO3<BR />
 +
 
}}
}}
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Cytochrome c nitrite reductase with 5 heme groups complex with NO2, acetate, Ca+2 ion (green) and Y+3 ion (cyan) (PDB code 2e80)

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3D structures of cytochrome c nitrite reductase

Updated on 02-March-2025

References

  1. ↑ Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, Kroneck PM. Structure of cytochrome c nitrite reductase. Nature. 1999 Jul 29;400(6743):476-80. PMID:10440380 doi:10.1038/22802
  2. ↑ Einsle O, Messerschmidt A, Huber R, Kroneck PM, Neese F. Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase. J Am Chem Soc. 2002 Oct 2;124(39):11737-45. PMID:12296741

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Michal Harel

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