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Protein

Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial

Gene

SDH3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Membrane-anchoring mono-heme cytochrome b subunit of succinate dehydrogenase (SDH) that is involved in system II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH3 and SDH4 form the membrane dimer that anchors the catalytic dimer formed by SDH1 and SDH2 to the matrix surface of the mitochondrial inner membrane. Electrons originating from the catalytic dimer enter the membrane dimer for ubiquinone reduction.

Cofactori

hemeNote: The heme is bound between the two transmembrane subunits.

Pathwayi: tricarboxylic acid cycle

This protein is involved in the pathway tricarboxylic acid cycle, which is part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei93 – 931UbiquinoneBy similarity
Binding sitei97 – 971UbiquinoneBy similarity
Metal bindingi156 – 1561Iron (heme axial ligand); shared with second transmembrane subunitBy similarity

GO - Molecular functioni

GO - Biological processi

  • cellular respiration Source: SGD
  • mitochondrial electron transport, succinate to ubiquinone Source: GO_Central
  • protein import into mitochondrial inner membrane Source: SGD
  • tricarboxylic acid cycle Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport, Tricarboxylic acid cycle

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:YKL141W-MONOMER.
YEAST:YKL141W-MONOMER.
UniPathwayiUPA00223.

Names & Taxonomyi

Protein namesi
Recommended name:
Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
Gene namesi
Name:SDH3
Synonyms:CYB3
Ordered Locus Names:YKL141W
ORF Names:YKL4
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL141W.
SGDiS000001624. SDH3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini51 – 9949Mitochondrial matrixSequence analysisAdd
BLAST
Transmembranei100 – 12021HelicalSequence analysisAdd
BLAST
Topological domaini121 – 13919Mitochondrial intermembraneSequence analysisAdd
BLAST
Transmembranei140 – 16021HelicalSequence analysisAdd
BLAST
Topological domaini161 – 17515Mitochondrial matrixSequence analysisAdd
BLAST
Transmembranei176 – 19621HelicalSequence analysisAdd
BLAST
Topological domaini197 – 1982Mitochondrial intermembraneSequence analysis

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Mitochondrion, Mitochondrion inner membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi96 – 961H → A or D: Decreases quinone reductase activity. 1 Publication
Mutagenesisi153 – 1531F → V: Decreases quinone reductase activity. Little effect on complex assembly. 1 Publication
Mutagenesisi156 – 1561H → A: Decreases SDH cytochrome b content. 1 Publication
Mutagenesisi163 – 1631H → Q: Decreases quinone reductase activity. Little effect on complex assembly. 1 Publication
Mutagenesisi166 – 1661W → R: Decreases quinone reductase activity. Little effect on complex assembly. 1 Publication
Mutagenesisi167 – 1671D → V: Reduces SDH FAD content. Probably impairs complex assembly.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 5050Mitochondrion1 PublicationAdd
BLAST
Chaini51 – 198148Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrialPRO_0000003638Add
BLAST

Keywords - PTMi

Quinone

Proteomic databases

MaxQBiP33421.

Interactioni

Subunit structurei

Forms part of complex II containing four subunits: a flavoprotein (FP), an iron-sulfur protein (IP) and a cytochrome b composed of two integral membrane proteins.

Protein-protein interaction databases

BioGridi33995. 61 interactions.
DIPiDIP-5310N.
IntActiP33421. 1 interaction.
MINTiMINT-502608.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ORZmodel-C51-198[»]
1PB4model-C51-198[»]
ProteinModelPortaliP33421.
SMRiP33421. Positions 68-191.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the cytochrome b560 family.Curated

Keywords - Domaini

Transit peptide, Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00840000131766.
HOGENOMiHOG000160253.
InParanoidiP33421.
KOiK00236.
OMAiAYAKSER.
OrthoDBiEOG725DVZ.

Family and domain databases

InterProiIPR018495. Succ_DH_cyt_bsu_CS.
IPR000701. Succ_DH_Fumarate_Rdtase_TM-su.
[Graphical view]
PfamiPF01127. Sdh_cyt. 1 hit.
[Graphical view]
PROSITEiPS01000. SDH_CYT_1. 1 hit.
PS01001. SDH_CYT_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P33421-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAMMVKLGL NKSALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK
60 70 80 90 100
NVASEMNTKA AIAEEQILNK QRAKRPISPH LTIYQPQLTW YLSSLHRISL
110 120 130 140 150
VLMGLGFYLF TILFGVSGLL GLGLTTEKVS NWYHQKFSKI TEWSIKGSFA
160 170 180 190
YLFAIHYGGA IRHLIWDTAK ELTLKGVYRT GYALIGFTAV LGTYLLTL
Length:198
Mass (Da):22,068
Last modified:February 1, 1994 - v1
Checksum:iF210FE99AE97607A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti10 – 101L → A in CAA52088 (PubMed:8195189).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z25464 Genomic DNA. Translation: CAA80957.1.
X73884 Genomic DNA. Translation: CAA52088.1.
Z28141 Genomic DNA. Translation: CAA81982.1.
AY693024 Genomic DNA. Translation: AAT93043.1.
BK006944 Genomic DNA. Translation: DAA09021.1.
PIRiS37970.
RefSeqiNP_012781.1. NM_001179707.1.

Genome annotation databases

EnsemblFungiiYKL141W; YKL141W; YKL141W.
GeneIDi853716.
KEGGisce:YKL141W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z25464 Genomic DNA. Translation: CAA80957.1.
X73884 Genomic DNA. Translation: CAA52088.1.
Z28141 Genomic DNA. Translation: CAA81982.1.
AY693024 Genomic DNA. Translation: AAT93043.1.
BK006944 Genomic DNA. Translation: DAA09021.1.
PIRiS37970.
RefSeqiNP_012781.1. NM_001179707.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ORZmodel-C51-198[»]
1PB4model-C51-198[»]
ProteinModelPortaliP33421.
SMRiP33421. Positions 68-191.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33995. 61 interactions.
DIPiDIP-5310N.
IntActiP33421. 1 interaction.
MINTiMINT-502608.

Proteomic databases

MaxQBiP33421.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL141W; YKL141W; YKL141W.
GeneIDi853716.
KEGGisce:YKL141W.

Organism-specific databases

EuPathDBiFungiDB:YKL141W.
SGDiS000001624. SDH3.

Phylogenomic databases

GeneTreeiENSGT00840000131766.
HOGENOMiHOG000160253.
InParanoidiP33421.
KOiK00236.
OMAiAYAKSER.
OrthoDBiEOG725DVZ.

Enzyme and pathway databases

UniPathwayiUPA00223.
BioCyciMetaCyc:YKL141W-MONOMER.
YEAST:YKL141W-MONOMER.

Miscellaneous databases

PROiP33421.

Family and domain databases

InterProiIPR018495. Succ_DH_cyt_bsu_CS.
IPR000701. Succ_DH_Fumarate_Rdtase_TM-su.
[Graphical view]
PfamiPF01127. Sdh_cyt. 1 hit.
[Graphical view]
PROSITEiPS01000. SDH_CYT_1. 1 hit.
PS01001. SDH_CYT_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning and physical analysis of an 8.2 kb segment of chromosome XI of Saccharomyces cerevisiae reveals five tightly linked genes."
    Abraham P.R., Mulder A., Van'T Riet J., Planta R.J., Raue H.A.
    Yeast 8:227-238(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Structure and regulation of SDH3, the yeast gene encoding the cytochrome b560 subunit of respiratory complex II."
    Daignan-Fornier B., Valens M., Lemire B.D., Bolotin-Fukuhara M.
    J. Biol. Chem. 269:15469-15472(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 51-79.
  3. "Complete DNA sequence of yeast chromosome XI."
    Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
    , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
    Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. "Characterization of the Saccharomyces cerevisiae nuclear gene CYB3 encoding a cytochrome b polypeptide of respiratory complex II."
    Abraham P.R., Mulder A., Van'T Riet J., Raue H.A.
    Mol. Gen. Genet. 242:708-716(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "The Saccharomyces cerevisiae succinate-ubiquinone oxidoreductase. Identification of Sdh3p amino acid residues involved in ubiquinone binding."
    Oyedotun K.S., Lemire B.D.
    J. Biol. Chem. 274:23956-23962(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF PHE-153; HIS-163 AND TRP-166.
  8. "The Saccharomyces cerevisiae mitochondrial succinate:ubiquinone oxidoreductase."
    Lemire B.D., Oyedotun K.S.
    Biochim. Biophys. Acta 1553:102-116(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW ON SUCCINATE DEHYDROGENASE.
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "Identification of the heme axial ligands in the cytochrome b562 of the Saccharomyces cerevisiae succinate dehydrogenase."
    Oyedotun K.S., Yau P.F., Lemire B.D.
    J. Biol. Chem. 279:9432-9439(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF HIS-96 AND HIS-156.
  11. "The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies."
    Oyedotun K.S., Lemire B.D.
    J. Biol. Chem. 279:9424-9431(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 51-198.

Entry informationi

Entry nameiSDH3_YEAST
AccessioniPrimary (citable) accession number: P33421
Secondary accession number(s): D6VX55
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: July 6, 2016
This is version 146 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 238 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.