Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  18 WHPVCALEDIWPNMGVCALIEGQQIAIFRLKDDQLYALDNHDPHSEANVLSRGLVGDLGGEPVVASPIYKHHYQLRTGVC 97
Cdd:cd03529    1 WQTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANVLSRGIVGDIGGEPVVASPLYKQHFSLKTGRC 80

                         90       100
                 ....*....|....*....|...
gi 902767630  98 VEDATVCLHVYPVEVRDGMVWVQ 120
Cdd:cd03529   81 LEDEDVSVATFPVRVEDGEVYVK 103

Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  18 WHPVCALEDIWPNMGVCALIEGQQIAIFRLKDDQLYALDNHDPHSEANVLSRGLVGDLGGEPVVASPIYKHHYQLRTGVC 97
Cdd:cd03529    1 WQTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANVLSRGIVGDIGGEPVVASPLYKQHFSLKTGRC 80

                         90       100
                 ....*....|....*....|...
gi 902767630  98 VEDATVCLHVYPVEVRDGMVWVQ 120
Cdd:cd03529   81 LEDEDVSVATFPVRVEDGEVYVK 103

nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused. [Central intermediary metabolism, Nitrogen metabolism]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630   18 WHPVCALEDIWPNMGVCALIEGQQIAIFRLKDDQLYALDNHDPHSEANVLSRGLVGDLGGEPVVASPIYKHHYQLRTGVC 97
Cdd:TIGR02378   2 WQDICAIDDIPEETGVCVLLGDTQIAIFRVPGDQVFAIQNMCPHKRAFVLSRGIVGDAQGELWVACPLHKRNFRLEDGRC 81

                          90       100
                  ....*....|....*....|....
gi 902767630   98 VEDATVCLHVYPVEVRDGMVWVQG 121
Cdd:TIGR02378  82 LEDDSGSVRTYEVRVEDGRVYVAL 105

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  17 AWHPVCALEDIWPNMGVCALIEGQQIAIFRLkDDQLYALDNHDPHSEANvLSRGLVGDLggepVVASPIYKHHYQLRTGV 96
Cdd:COG2146    2 SEVKVCALDDLPEGGGVVVEVGGKQIAVFRT-DGEVYAYDNRCPHQGAP-LSEGIVDGG----VVTCPLHGARFDLRTGE 75

                         90       100
                 ....*....|....*....|....
gi 902767630  97 CVE-DATVCLHVYPVEVRDGMVWV 119
Cdd:COG2146   76 CLGgPATEPLKTYPVRVEDGDVYV 99

Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  18 WHPVCALEDIWPNMGVCALIEGQQIAIFRLKDDQLYALDNHDPHSEANVLSRGLVGDLGGEPVVASPIYKHHYQLRTGVC 97
Cdd:cd03529    1 WQTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANVLSRGIVGDIGGEPVVASPLYKQHFSLKTGRC 80

                         90       100
                 ....*....|....*....|...
gi 902767630  98 VEDATVCLHVYPVEVRDGMVWVQ 120
Cdd:cd03529   81 LEDEDVSVATFPVRVEDGEVYVK 103

nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused. [Central intermediary metabolism, Nitrogen metabolism]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630   18 WHPVCALEDIWPNMGVCALIEGQQIAIFRLKDDQLYALDNHDPHSEANVLSRGLVGDLGGEPVVASPIYKHHYQLRTGVC 97
Cdd:TIGR02378   2 WQDICAIDDIPEETGVCVLLGDTQIAIFRVPGDQVFAIQNMCPHKRAFVLSRGIVGDAQGELWVACPLHKRNFRLEDGRC 81

                          90       100
                  ....*....|....*....|....
gi 902767630   98 VEDATVCLHVYPVEVRDGMVWVQG 121
Cdd:TIGR02378  82 LEDDSGSVRTYEVRVEDGRVYVAL 105

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  17 AWHPVCALEDIWPNMGVCALIEGQQIAIFRLkDDQLYALDNHDPHSEANvLSRGLVGDLggepVVASPIYKHHYQLRTGV 96
Cdd:COG2146    2 SEVKVCALDDLPEGGGVVVEVGGKQIAVFRT-DGEVYAYDNRCPHQGAP-LSEGIVDGG----VVTCPLHGARFDLRTGE 75

                         90       100
                 ....*....|....*....|....
gi 902767630  97 CVE-DATVCLHVYPVEVRDGMVWV 119
Cdd:COG2146   76 CLGgPATEPLKTYPVRVEDGDVYV 99

Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the insertions that give other Rieske proteins unique structural features are missing. CARDO catalyzes dihydroxylation at the C1 and C9a positions of carbazole. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  18 WHPVCALEDIWPNMGVCALIEGQQIAIFRLkDDQLYALDNHDPHSEANvLSRGLVGDLggepVVASPIYKHHYQLRTGVC 97
Cdd:cd03528    1 WVRVCAVDELPEGEPKRVDVGGRPIAVYRV-DGEFYATDDLCTHGDAS-LSEGYVEGG----VIECPLHGGRFDLRTGKA 74

                         90       100
                 ....*....|....*....|...
gi 902767630  98 V-EDATVCLHVYPVEVRDGMVWV 119
Cdd:cd03528   75 LsLPATEPLKTYPVKVEDGDVYV 97

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630   17 AWHPVCALEDIWPNMGVCALIEGQQIAIFRLKDDQLYALDNHDPHSEANvLSRGLVGDLG 76
Cdd:pfam00355   1 SWYPVCHSSELPEGEPKVVEVGGEPLVVFRDEDGELYALEDRCPHRGAP-LSEGKVNGGG 59

Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the initial source of two electrons for dioxygen activation.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  18 WHPVCALEDIwPNMG--VCALIEGQQIAIFRLKDDQLYALDNHDPHsEANVLSRGLVG--------------DLGGEpVV 81
Cdd:cd03469    1 WYFVGHSSEL-PEPGdyVTLELGGEPLVLVRDRDGEVRAFHNVCPH-RGARLCEGRGGnagrlvcpyhgwtyDLDGK-LV 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 902767630  82 ASPiykhhyQLRTGVCVEDATVCLHVYPVEVRDGMVWV 119
Cdd:cd03469   78 GVP------REEGFPGFDKEKLGLRTVPVEEWGGLIFV 109

AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902767630  50 DQLYALDNHDPHSEANvLSRGLVGDlggePVVASPIYKHHYQLRTGVCVE-DATVCLHVYPVEVRDGMVW 118
Cdd:cd03478   31 GEVHAIGAKCPHYGAP-LAKGVLTD----GRIRCPWHGACFNLRTGDIEDaPALDSLPCYEVEVEDGRVY 95