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Conserved domains on  [gi|410697620|gb|AFV76688|]
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succinate dehydrogenase, cytochrome b556 subunit [Thermus oshimai JL-2]

Protein Classification

succinate dehydrogenase, cytochrome b556 subunit( domain architecture ID 10131285)

succinate dehydrogenase, cytochrome b556 subunit (also called the C subunit), together with the D subunit, acts to anchor the catalytic components of succinate dehydrogenase to the cytoplasmic membrane

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SQR_TypeA_SdhC_like cd03501
Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like ...
 8-106 2.70e-36

Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial SQRs, which contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


:

Pssm-ID: 239581  Cd Length: 101  Bit Score: 119.30  E-value: 2.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620   8 QWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFTAWGVRY 87
Cdd:cd03501    1 MWAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVFHALNGIRLILVDFGSGGPRY 80

                         90
                 ....*....|....*....
gi 410697620  88 QRALWYGVWVLFVVFYLPF 106
Cdd:cd03501   81 QRQLFYIVLVLTVVLIVAA 99
 
Name Accession Description Interval E-value
SQR_TypeA_SdhC_like cd03501
Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like ...
 8-106 2.70e-36

Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial SQRs, which contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


Pssm-ID: 239581  Cd Length: 101  Bit Score: 119.30  E-value: 2.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620   8 QWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFTAWGVRY 87
Cdd:cd03501    1 MWAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVFHALNGIRLILVDFGSGGPRY 80

                         90
                 ....*....|....*....
gi 410697620  88 QRALWYGVWVLFVVFYLPF 106
Cdd:cd03501   81 QRQLFYIVLVLTVVLIVAA 99
SdhC COG2009
Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and ...
 2-101 4.69e-16

Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion];


Pssm-ID: 441612  Cd Length: 128  Bit Score: 68.65  E-value: 4.69e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620   2 YRGREGQWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFT 81
Cdd:COG2009   16 YRLPLTMIVSILHRITGVALFLGLPLLVWWLAASASSPEAFAAVQAFLGSPLGKLVLLGLTWALLYHLLAGIRHLLWDFG 95

                         90       100
                 ....*....|....*....|.
gi 410697620  82 AW-GVRYQRALWYGVWVLFVV 101
Cdd:COG2009   96 YGfELETARRSAWVVLVLSVV 116
succ_dehyd_cytB TIGR02970
succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two ...
 2-102 3.07e-11

succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see TIGR02046). [Energy metabolism, TCA cycle]


Pssm-ID: 274370  Cd Length: 120  Bit Score: 56.04  E-value: 3.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620    2 YRGREGQWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFT 81
Cdd:TIGR02970  12 YRFPITAILSILHRITGVLLFFGLPFLLWWLSLSLSSPESFATVHALLSSPLGKLILWGLLWALLYHLLAGIRHLLWDLG 91

                          90       100
                  ....*....|....*....|..
gi 410697620   82 AW-GVRYQRALWYGVWVLFVVF 102
Cdd:TIGR02970  92 YGlELKSARISAWVVLVLSLVL 113
Sdh_cyt pfam01127
Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a ...
 1-102 1.92e-07

Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.


Pssm-ID: 426067  Cd Length: 122  Bit Score: 46.22  E-value: 1.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620    1 MYRGREGQWAFYLHRISGLGILVFLILHILNIG---SAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIIL 77
Cdd:pfam01127  13 LYRAHLTTWLSILHRITGVALAVLGLIFLLLWLlllLSLLGPESYATVVAWLASPVKLILLLLLLLALFYHAANGIRHLI 92

                          90       100
                  ....*....|....*....|....*
gi 410697620   78 MDFTAWGVRYQRALWYGVWVLFVVF 102
Cdd:pfam01127  93 WDVGFGLELKTVRKSGAAVLALSVV 117
 
Name Accession Description Interval E-value
SQR_TypeA_SdhC_like cd03501
Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like ...
 8-106 2.70e-36

Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial SQRs, which contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


Pssm-ID: 239581  Cd Length: 101  Bit Score: 119.30  E-value: 2.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620   8 QWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFTAWGVRY 87
Cdd:cd03501    1 MWAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVFHALNGIRLILVDFGSGGPRY 80

                         90
                 ....*....|....*....
gi 410697620  88 QRALWYGVWVLFVVFYLPF 106
Cdd:cd03501   81 QRQLFYIVLVLTVVLIVAA 99
SdhC COG2009
Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and ...
 2-101 4.69e-16

Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion];


Pssm-ID: 441612  Cd Length: 128  Bit Score: 68.65  E-value: 4.69e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620   2 YRGREGQWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFT 81
Cdd:COG2009   16 YRLPLTMIVSILHRITGVALFLGLPLLVWWLAASASSPEAFAAVQAFLGSPLGKLVLLGLTWALLYHLLAGIRHLLWDFG 95

                         90       100
                 ....*....|....*....|.
gi 410697620  82 AW-GVRYQRALWYGVWVLFVV 101
Cdd:COG2009   96 YGfELETARRSAWVVLVLSVV 116
succ_dehyd_cytB TIGR02970
succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two ...
 2-102 3.07e-11

succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see TIGR02046). [Energy metabolism, TCA cycle]


Pssm-ID: 274370  Cd Length: 120  Bit Score: 56.04  E-value: 3.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620    2 YRGREGQWAFYLHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFT 81
Cdd:TIGR02970  12 YRFPITAILSILHRITGVLLFFGLPFLLWWLSLSLSSPESFATVHALLSSPLGKLILWGLLWALLYHLLAGIRHLLWDLG 91

                          90       100
                  ....*....|....*....|..
gi 410697620   82 AW-GVRYQRALWYGVWVLFVVF 102
Cdd:TIGR02970  92 YGlELKSARISAWVVLVLSLVL 113
SQR_QFR_TM cd03493
Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, ...
 13-106 7.70e-08

Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQRs may reduce either high or low potential quinones while QFRs oxidize only low potential quinols. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit(s) containing the electron donor/acceptor (quinol or quinone). The reversible reduction of quinone is an essential feature of respiration, allowing the transfer of electrons between respiratory complexes. SQRs and QFRs can be classified into five types (A-E) according to the number of their hydrophobic subunits and heme groups. This classification is consistent with the characteristics and phylogeny of the catalytic and iron-sulfur subunits. Type E proteins, e.g. non-classical archael SQRs, contain atypical transmembrane subunits and are not included in this hierarchy. The heme and quinone binding sites reside in the transmembrane subunits. Although succinate oxidation and fumarate reduction are carried out by separate enzymes in most organisms, some bifunctional enzymes that exhibit both SQR and QFR activities exist.


Pssm-ID: 239573  Cd Length: 98  Bit Score: 46.51  E-value: 7.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620  13 LHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFTAW-GVRYQRAL 91
Cdd:cd03493    2 LHRITGVALLLFLPLHLLGLLALLGGPYAFAEVVAFLSSPLGKLLYLLLLLALLYHALNGIRHLIWDYGKGlELKLRKAL 81

                         90
                 ....*....|....*
gi 410697620  92 WYGVWVLFVVFYLPF 106
Cdd:cd03493   82 GYAVLALSVLLTVLL 96
Sdh_cyt pfam01127
Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a ...
 1-102 1.92e-07

Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.


Pssm-ID: 426067  Cd Length: 122  Bit Score: 46.22  E-value: 1.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620    1 MYRGREGQWAFYLHRISGLGILVFLILHILNIG---SAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIIL 77
Cdd:pfam01127  13 LYRAHLTTWLSILHRITGVALAVLGLIFLLLWLlllLSLLGPESYATVVAWLASPVKLILLLLLLLALFYHAANGIRHLI 92

                          90       100
                  ....*....|....*....|....*
gi 410697620   78 MDFTAWGVRYQRALWYGVWVLFVVF 102
Cdd:pfam01127  93 WDVGFGLELKTVRKSGAAVLALSVV 117
SdhD COG2142
Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];
3-79 2.96e-07

Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];


Pssm-ID: 441745  Cd Length: 124  Bit Score: 45.59  E-value: 2.96e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 410697620   3 RGREGQWAFYLHRISGLGILVFLILHIlniGSAMWGPEVS-NALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMD 79
Cdd:COG2142   15 SAKSGTHHWLLQRVTAVALVVLVLWFL---FFLLSLPGADyAEVAAWFASPFWAILTLLFLLSALYHAWLGLRVVIED 89
SQR_TypeA_SdhD_like cd03500
Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase D (SdhD)-like ...
 7-101 1.30e-05

Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase D (SdhD)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial SQRs, which contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


Pssm-ID: 239580  Cd Length: 106  Bit Score: 41.11  E-value: 1.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 410697620   7 GQWAFYLHRISGLGILVFLILHILNigSAMWGPEVS---NALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDFTAw 83
Cdd:cd03500    1 ESLAWLFQRITGVFLVFLLAGHFWV--QHMDNGGDVidfAFVANRLASPLWKVWDLLLLVLALLHGGNGLRNILLDYVR- 77

                         90
                 ....*....|....*...
gi 410697620  84 GVRYQRALWYGVWVLFVV 101
Cdd:cd03500   78 RPRLRRAVKGLLYVAGLL 95
SQR_TypeC_SdhC cd03499
Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) ...
 13-80 4.08e-05

Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


Pssm-ID: 239579  Cd Length: 117  Bit Score: 39.83  E-value: 4.08e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 410697620  13 LHRISGLGILVFLILHILNIGSAMWGPEVSNALMKFYHQPVFQLGLLLLIAGVLYHGFNGLRIILMDF 80
Cdd:cd03499   21 LHRITGVALFLGLPLLLWWLLASLSSPESFESVSALLGSWLGKLVLFGLTWALFYHLLNGIRHLIWDL 88
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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