Nitrite reductase: Difference between revisions

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<StructureSection load='Cca.pdb' size='350' side='right' scene='Journal:JBIC:16/Cv/2' caption='Heme-containing nitrite reductase with heme and Ca+2 ions (PDB code [[3ubr]])'>
<StructureSection load='Cca.pdb' size='350' side='right' scene='Journal:JBIC:16/Cv/2' caption='Heme-containing nitrite reductase with heme and Ca+2 ions (PDB code [[3ubr]])'>
__TOC__
==Function==
'''Nitrite reductase''' (NIR) catalyzes the reduction of NO<sub>2</sub> to NO.  There are 2 classes of NIR: (1) A '''heme-containing cytochrome Cd type NIR'''.  This enzyme contains 4 heme groups.  Its d-type heme group binds NO<sub>2</sub>.  (2) A '''copper-containing NIR''' which produces NO<sub>2</sub>.  Under anaerobic conditions bacteria rely on the reduction of nitrogen oxide species to obtain energy.  NIR is part of the nitrogen cycle used for this purpose.
'''Nitrite reductase''' (NIR) catalyzes the reduction of NO<sub>2</sub> to NO.  There are 2 classes of NIR: (1) A '''heme-containing cytochrome Cd type NIR'''.  This enzyme contains 4 heme groups.  Its d-type heme group binds NO<sub>2</sub>.  (2) A '''copper-containing NIR''' which produces NO<sub>2</sub>.  Under anaerobic conditions bacteria rely on the reduction of nitrogen oxide species to obtain energy.  NIR is part of the nitrogen cycle used for this purpose.


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</StructureSection>
</StructureSection>


==3D structures of nitrite reductase==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
*'''Cu-containing nitrite reductase with copper only'''
**[[1nia]], [[1nib]], [[1nic]], [[1nid]], [[1nie]], [[1nif]], [[2nrd]], [[1kcb]], [[1rzp]], [[1rzq]], [[2bw4]], [[2bw5]], [[2avf]], [[5l6k]], [[5i6l]], [[5l6m]], [[5i6n]], [[5l6o]], [[5i6p]], [[5n8f]], [[5n8g]], [[5n8h]], [[5n8i]],  [[6gsq]], [[6gt2]], [[6gtj]] – AcNIR + Cu – ''Achromobacter cycloclastes''<br />
**[[2afn]], [[1aq8]], [[1as7]], [[2fjs]], [[2pp7]], [[2pp8]], [[3h4h]], [[3h56]], [[4ysc]], [[4yse]], [[5d4h]], [[5d4i]], [[5d4j]], [[5f7a]], [[5f7b]]  - AfNIR + Cu – ''Alcaligenes faecalis''<br />
**[[1ntd]], [[1npj]], [[1npn]], [[1zdq]], [[3h4f]] - AfNIR (mutant) + Cu<br />
**[[1ndr]], [[1ndt]], [[1bq5]], [[1hau]], [[1haw]], [[1oe1]], [[1oe3]], [[5b1k]] - AxNIR + Cu – ''Achromobacter xylosoxidans''<br />
**[[1oe2]], [[2jfc]] - AxNIR (mutant) + Cu<br />
**[[1mzz]], [[2dy2]] - RsNIR + Cu – ''Rhodobacter sphaeroides''<br />
**[[2dv6]] - NIR + Cu – ''Hyphomicrobium denitrificans''<br />
**[[3wia]] - GkNIR + Cu – ''Geobacillus kaustophilus''<br />
**[[3wkq]], [[3x1e]], [[4ysa]], [[4ysd]], [[4yso]], [[4ysp]], [[4ysq]], [[4ysr]], [[4yss]], [[4yst]], [[4ysu]], [[4zk8]], [[5ytl]] - GtNIR + Cu - ''Geobacillus thermodentntrificans''<br />
**[[3x1f]], [[3x1g]] - GtNIR (mutant) + Cu <br />
**[[5tb7]], [[5ue6]] - NIR + Cu – ''Neisseria gonorrhoeae''<br />
**[[6hbe]] - NIR + Cu – ''Thermus scotoductus''<br />
**[[6qpu]] – RpNIR + Cu – ''Ralstonia pickettii''<br />
*Cu-containing nitrite reductase with variety of metals
**[[1et5]], [[1et8]] - AfNIR (mutant) + Zn + Cu<br />
**[[1et7]] - AfNIR (mutant) + Cd + Cu<br />
**[[2vm3]], [[2vm4]], [[2vw4]], [[2vw6]], [[2vw7]], [[2vn3]] - AxNIR + Zn + Cu<br />
**[[2bo0]] - AxNIR (mutant) + Zn<br />
**[[2vmj]] - AxNIR + Zn <br />
**[[1gs6]] - AxNIR (mutant) + Mg + Cu<br />
**[[1gs7]], [[1wae]], [[1wa0]], [[1wa1]], [[2bp0]], [[2bp8]], [[2xx0]], [[2xxf]], [[2xxg]] - AxNIR (mutant) + Zn + Cu<br />
**[[2zon]] - AxNIR + heme + Cu<br />
**[[1mzy]], [[1zv2]], [[2a3t]] - RsNIR + Mg + Cu<br />
**[[1n70]] - RsNIR (mutant) + Mg + Cu<br />
**[[3wi9]] - GkNIR + Zn + Cu <br />
**[[5onx]], [[5ony]] - NIR + Zn + Cu – ''Alcaligenes xylosoxydans''<br />
*Cu-containing nitrite reductase binary complex
**[[1as6]], [[1as8]], [[1sjm]], [[2ppc]] - AfNIR + NO2 + Cu<br />
**[[2e86]] - AfNIR + N3 + Cu<br />
**[[1j9q]], [[1j9r]], [[1j9s]], [[1j9t]], [[1l9o]], [[1l9p]], [[1l9q]], [[1l9r]], [[1l9s]], [[1l9t]] - AfNIR (mutant) + NO2 + Cu<br />
**[[1zds]], [[2b08]] - AfNIR (mutant) + acetamide + Cu<br />
**[[1snr]] - AfNIR + NO + Cu<br />
**[[2pp9]] - AfNIR + NO3 + Cu<br />
**[[2ppa]] - AfNIR + N2O + Cu<br />
**[[2ppd]], [[2ppe]], [[2ppf]] - AfNIR (mutant) + NO + Cu<br />
**[[2p80]] - AfNIR + pseudoazurin + Cu<br />
**[[1nds]] - AxNIR + NO2 + Cu<br />
**[[2xx1]] - AxNIR (mutant) + NO2 + Cu<br />
**[[2xwz]] - AxNIR + NO + NO2 + Cu<br />
**[[1wa2]] - AxNIR (mutant) + NO2 + Zn + Cu<br />
**[[5b1j]] - AxNIR + pseudoazurin + Cu <br />
**[[2bwd]], [[2bwi]], [[5og2]], [[5og3]], [[5og4]], [[5og5]], [[5og6]], [[5ogf]], [[5ogg]], [[5of5]], [[5of6]], [[5of7]], [[5of8]], [[5ofc]], [[5ofd]], [[5ofe]], [[5off]], [[5ofg]], [[5ofh]], [[5i6k]], [[5i6m]], [[5i6o]], [[5akr]], [[6gb8]], [[6gbb]], [[6gby]], [[6gcg]], [[6gt0]], [[6gti]], [[6gtk]], [[6gtl]], [[6gtn]] - AcNIR + NO2 + Cu<br />
**[[4csz]] - AcNIR (mutant) + NO2 + Cu <br />
**[[4csp]] - AcNIR (mutant) + Zn + Cu <br />
**[[2y1a]] - AcNIR + NO + Cu<br />
**[[2dws]], [[2dwt]] - RsNIR + NO2 + Cu<br />
**[[3wkp]], [[3x1n]] - GtNIR (mutant) + NO2 + Cu <br />
**[[3wni]], [[3wnj]] - GtNIR + O2 + Cu <br />
**[[5ytn]] - GtNIR (mutant) + H2O2 + Cu <br />
**[[6qpt]] – RpNIR + Cu + NO2 <br />
**[[6qpv]], [[6qpz]], [[6qq1]] – RpNIR (mutant) + Cu + heme <br />
**[[6qpx]], [[6qq0]], [[6qq2]] – RpNIR (mutant) + Cu + heme + NO2<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]] – 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]] – SoNIR – ''Shewanella oneidensis''<br />
**[[3sqx]] – TpNIR – ''Thioalkalivibrio paradoxus''<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
*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 />
*'''Siroheme-containing assimilatory nitrite reductase'''
**[[2akj]] - NIR + S4Fe4 + siroheme – spinach<br />
**[[3b0g]], [[3b0h]] - ToNIR + S4Fe4 + siroheme – tobacco<br />
**[[3b0j]], [[3b0l]], [[3b0m]], [[3b0n]], [[3vlx]], [[3vly]], [[3vlz]]  - ToNIR (mutant) + S4Fe4 + siroheme <br />
**[[3vkp]], [[3vkq]], [[3vkr]] – SToNIR + S4Fe4 + siroheme + NO2<br />
**[[3vm0]] – SToNIR (mutant) + S4Fe4 + siroheme + NO2<br />
**[[3vm1]] – SToNIR (mutant) + S4Fe4 + siroheme + HCO3<br />
**[[3vks]] – SToNIR + S4Fe4 + siroheme + NO<br />
**[[3vkt]] – SToNIR + S4Fe4 + siroheme + NH2OH<br />
}}
'''References'''
'''References'''
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]
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