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Conserved domains on  [gi|322812301|pdb|3AE9|D]
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Chain D, Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

Protein Classification

SQR_TypeC_CybS domain-containing protein( domain architecture ID 10131270)

SQR_TypeC_CybS domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SQR_TypeC_CybS cd03496
SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to ...
 4-102 4.41e-35

SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs 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. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homolog of the bacterial SdhD subunit. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane 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. Mutations in human Complex II result in various physiological disorders including hereditary paraganglioma and pheochromocytoma tumors. The gene encoding for the SdhD subunit is classified as a tumor suppressor gene.


:

Pssm-ID: 239576  Cd Length: 104  Bit Score: 115.80  E-value: 4.41e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AE9_D        4 KAASLHWTGERVVSVLLLGLLPAAYLNP--CSAMDYSLAAALTLHGHWGIGQVVTDYVR---GDALQKAAKAGLLALSAF 78
Cdd:cd03496   1 LHGSYHWTFERILAVSLLPLTPAAFFAPglSPVMDAALAAALLLHSHWGFESCIIDYVPkrvGGKLHKLAMYLLYAGSAL 80

                        90       100
                ....*....|....*....|....
3AE9_D       79 TFAGLCYFNYHDVGICKAVAMLWK 102
Cdd:cd03496  81 SLAGLYYFNTNDVGLTKAVKKLWS 104
 
Name Accession Description Interval E-value
SQR_TypeC_CybS cd03496
SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to ...
 4-102 4.41e-35

SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs 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. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homolog of the bacterial SdhD subunit. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane 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. Mutations in human Complex II result in various physiological disorders including hereditary paraganglioma and pheochromocytoma tumors. The gene encoding for the SdhD subunit is classified as a tumor suppressor gene.


Pssm-ID: 239576  Cd Length: 104  Bit Score: 115.80  E-value: 4.41e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AE9_D        4 KAASLHWTGERVVSVLLLGLLPAAYLNP--CSAMDYSLAAALTLHGHWGIGQVVTDYVR---GDALQKAAKAGLLALSAF 78
Cdd:cd03496   1 LHGSYHWTFERILAVSLLPLTPAAFFAPglSPVMDAALAAALLLHSHWGFESCIIDYVPkrvGGKLHKLAMYLLYAGSAL 80

                        90       100
                ....*....|....*....|....
3AE9_D       79 TFAGLCYFNYHDVGICKAVAMLWK 102
Cdd:cd03496  81 SLAGLYYFNTNDVGLTKAVKKLWS 104
CybS pfam05328
CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several ...
 7-102 4.44e-18

CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularised tumours in the head and neck.


Pssm-ID: 461624  Cd Length: 131  Bit Score: 73.04  E-value: 4.44e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AE9_D          7 SLHWTGERVVSVLLLGLLPAAYL--NPCSAMDYSLAAALTLHGHWGIGQVVTDYVRGD---ALQKAAKAGLLALSAFTFA 81
Cdd:pfam05328  31 SYHWTFERIVAVGLLPLTPAPFAagSPSPVLDAVLASSLLGHCHIGFQSCIIDYIPKRvygKWHKAAMYLLYLGTGVSLY 110

                          90       100
                  ....*....|....*....|.
3AE9_D         82 GLCYFNYHDVGICKAVAMLWK 102
Cdd:pfam05328 111 GLYELETNDNGLTELVKKLWS 131
 
Name Accession Description Interval E-value
SQR_TypeC_CybS cd03496
SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to ...
 4-102 4.41e-35

SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs 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. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homolog of the bacterial SdhD subunit. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane 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. Mutations in human Complex II result in various physiological disorders including hereditary paraganglioma and pheochromocytoma tumors. The gene encoding for the SdhD subunit is classified as a tumor suppressor gene.


Pssm-ID: 239576  Cd Length: 104  Bit Score: 115.80  E-value: 4.41e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AE9_D        4 KAASLHWTGERVVSVLLLGLLPAAYLNP--CSAMDYSLAAALTLHGHWGIGQVVTDYVR---GDALQKAAKAGLLALSAF 78
Cdd:cd03496   1 LHGSYHWTFERILAVSLLPLTPAAFFAPglSPVMDAALAAALLLHSHWGFESCIIDYVPkrvGGKLHKLAMYLLYAGSAL 80

                        90       100
                ....*....|....*....|....
3AE9_D       79 TFAGLCYFNYHDVGICKAVAMLWK 102
Cdd:cd03496  81 SLAGLYYFNTNDVGLTKAVKKLWS 104
CybS pfam05328
CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several ...
 7-102 4.44e-18

CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularised tumours in the head and neck.


Pssm-ID: 461624  Cd Length: 131  Bit Score: 73.04  E-value: 4.44e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AE9_D          7 SLHWTGERVVSVLLLGLLPAAYL--NPCSAMDYSLAAALTLHGHWGIGQVVTDYVRGD---ALQKAAKAGLLALSAFTFA 81
Cdd:pfam05328  31 SYHWTFERIVAVGLLPLTPAPFAagSPSPVLDAVLASSLLGHCHIGFQSCIIDYIPKRvygKWHKAAMYLLYLGTGVSLY 110

                          90       100
                  ....*....|....*....|.
3AE9_D         82 GLCYFNYHDVGICKAVAMLWK 102
Cdd:pfam05328 111 GLYELETNDNGLTELVKKLWS 131
SQR_QFR_TM cd03493
Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, ...
 34-85 6.54e-03

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: 33.02  E-value: 6.54e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
3AE9_D       34 AMDYSLAAALTLHGHWGIGQVVTDYVRGD--ALQKAAKAGLLALSAFTFAGLCY 85
Cdd:cd03493  45 LLYLLLLLALLYHALNGIRHLIWDYGKGLelKLRKALGYAVLALSVLLTVLLLF 98
 
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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