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Cytochrome c nitrite reductase: Difference between revisions

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<StructureSection load='2e80' size='340' side='right' caption='Cytochrome c nitrite reductase with 5 heme groups complex with NO2, acetate Ca+2 ion (green) and Y+3 ion (cyan) (PDB code [[2e80]])' scene='83/833267/Cv/3'>
<StructureSection load='2e80' size='340' side='right' caption='Cytochrome c nitrite reductase with 5 heme groups complex with NO2, acetate, Ca+2 ion (green) and Y+3 ion (cyan) (PDB code [[2e80]])' scene='83/833267/Cv/3'>
   
   
== Function ==
== Function ==
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'''Cytochrome c nitrite reductase''' or '''cytochrome c552''' (ccNiR) catalyzes the reduction of nitrite to ammonia as one of the key steps in the nitrogen cycle where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification<ref>PMID:10440380</ref>.
'''Cytochrome c nitrite reductase''' or '''cytochrome c552''' (ccNiR) catalyzes the reduction of nitrite to ammonia as one of the key steps in the nitrogen cycle where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification<ref>PMID:10440380</ref>.


See also [[Hemeproteins]].
See also [[Hemeproteins#Cytochrome c Nitrite Reductase|Hemeproteins: Cytochrome c Nitrite Reductase]].


== Structural highlights ==
== Structural highlights ==


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.
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]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky
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