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Succinate dehydrogenase iron-sulfur subunit (EC 1.3.5.1)

 SDHB_ECOLI              Reviewed;         238 AA.
P07014;
01-APR-1988, integrated into UniProtKB/Swiss-Prot.
01-APR-1988, sequence version 1.
05-DEC-2018, entry version 173.
RecName: Full=Succinate dehydrogenase iron-sulfur subunit;
EC=1.3.5.1;
Name=sdhB; OrderedLocusNames=b0724, JW0714;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=6388571; DOI=10.1042/bj2230507;
Darlison M.G., Guest J.R.;
"Nucleotide sequence encoding the iron-sulphur protein subunit of the
succinate dehydrogenase of Escherichia coli.";
Biochem. J. 223:507-517(1984).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8905232; DOI=10.1093/dnares/3.3.137;
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
Yano M., Horiuchi T.;
"A 718-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 12.7-28.0 min region on the linkage map.";
DNA Res. 3:137-155(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 231-238.
PubMed=6376123; DOI=10.1111/j.1432-1033.1984.tb08199.x;
Darlison M.G., Spencer M.E., Guest J.R.;
"Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate
dehydrogenase of Escherichia coli K12.";
Eur. J. Biochem. 141:351-359(1984).
[6]
PROTEIN SEQUENCE OF 1-11.
STRAIN=K12 / EMG2;
PubMed=9298646; DOI=10.1002/elps.1150180807;
Link A.J., Robison K., Church G.M.;
"Comparing the predicted and observed properties of proteins encoded
in the genome of Escherichia coli K-12.";
Electrophoresis 18:1259-1313(1997).
[7]
SUBUNIT, AND SUBCELLULAR LOCATION.
STRAIN=BL21-DE3;
PubMed=16079137; DOI=10.1074/jbc.M506479200;
Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L.,
von Heijne G., Daley D.O.;
"Protein complexes of the Escherichia coli cell envelope.";
J. Biol. Chem. 280:34409-34419(2005).
[8]
X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
CLUSTERS AND UBIQUINONE, COFACTOR, AND SUBUNIT.
PubMed=12560550; DOI=10.1126/science.1079605;
Yankovskaya V., Horsefield R., Toernroth S., Luna-Chavez C.,
Miyoshi H., Leger C., Byrne B., Cecchini G., Iwata S.;
"Architecture of succinate dehydrogenase and reactive oxygen species
generation.";
Science 299:700-704(2003).
[9]
X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
CLUSTERS, COFACTOR, AND SUBUNIT.
PubMed=16407191; DOI=10.1074/jbc.M508173200;
Horsefield R., Yankovskaya V., Sexton G., Whittingham W., Shiomi K.,
Omura S., Byrne B., Cecchini G., Iwata S.;
"Structural and computational analysis of the quinone-binding site of
complex II (succinate-ubiquinone oxidoreductase): a mechanism of
electron transfer and proton conduction during ubiquinone reduction.";
J. Biol. Chem. 281:7309-7316(2006).
[10]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
CLUSTERS, COFACTOR, AND SUBUNIT.
PubMed=19710024; DOI=10.1074/jbc.M109.010058;
Ruprecht J., Yankovskaya V., Maklashina E., Iwata S., Cecchini G.;
"Structure of Escherichia coli succinate:quinone oxidoreductase with
an occupied and empty quinone-binding site.";
J. Biol. Chem. 284:29836-29846(2009).
-!- FUNCTION: Two distinct, membrane-bound, FAD-containing enzymes are
responsible for the catalysis of fumarate and succinate
interconversion; the fumarate reductase is used in anaerobic
growth, and the succinate dehydrogenase is used in aerobic growth.
-!- CATALYTIC ACTIVITY:
Reaction=a quinone + succinate = a quinol + fumarate;
Xref=Rhea:RHEA:40523, ChEBI:CHEBI:24646, ChEBI:CHEBI:29806,
ChEBI:CHEBI:30031, ChEBI:CHEBI:132124; EC=1.3.5.1;
-!- COFACTOR:
Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:49601;
Note=Binds 1 [2Fe-2S] cluster.;
-!- COFACTOR:
Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
Note=Binds 1 [3Fe-4S] cluster.;
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Note=Binds 1 [4Fe-4S] cluster.;
-!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle;
fumarate from succinate (bacterial route): step 1/1.
-!- SUBUNIT: Part of an enzyme complex containing four subunits: a
flavoprotein, an iron-sulfur, cytochrome b-556, and a hydrophobic
anchor protein. The complex forms trimers.
{ECO:0000269|PubMed:12560550, ECO:0000269|PubMed:16079137,
ECO:0000269|PubMed:16407191, ECO:0000269|PubMed:19710024}.
-!- INTERACTION:
P0AC41:sdhA; NbExp=2; IntAct=EBI-1035514, EBI-371263;
-!- SUBCELLULAR LOCATION: Cell inner membrane
{ECO:0000269|PubMed:16079137}; Peripheral membrane protein
{ECO:0000269|PubMed:16079137}.
-!- SIMILARITY: Belongs to the succinate dehydrogenase/fumarate
reductase iron-sulfur protein family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; J01619; AAA23896.1; -; Genomic_DNA.
EMBL; X01070; CAA25534.1; -; Genomic_DNA.
EMBL; U00096; AAC73818.1; -; Genomic_DNA.
EMBL; AP009048; BAA35391.1; -; Genomic_DNA.
EMBL; X00661; CAA25279.1; -; Genomic_DNA.
PIR; A28837; DEECSI.
RefSeq; NP_415252.1; NC_000913.3.
RefSeq; WP_001235254.1; NZ_LN832404.1.
PDB; 1NEK; X-ray; 2.60 A; B=1-238.
PDB; 1NEN; X-ray; 2.90 A; B=1-238.
PDB; 2ACZ; X-ray; 3.10 A; B=1-238.
PDB; 2AD0; Model; -; B=1-238.
PDB; 2WDQ; X-ray; 2.40 A; B/F/J=1-238.
PDB; 2WDR; X-ray; 3.20 A; B/F/J=1-238.
PDB; 2WDV; X-ray; 3.20 A; B/F/J=1-238.
PDB; 2WP9; X-ray; 2.70 A; B/F/J=1-238.
PDB; 2WS3; X-ray; 3.20 A; B/F/J=1-238.
PDB; 2WU2; X-ray; 2.50 A; B/F/J=1-238.
PDB; 2WU5; X-ray; 2.80 A; B/F/J=1-238.
PDBsum; 1NEK; -.
PDBsum; 1NEN; -.
PDBsum; 2ACZ; -.
PDBsum; 2AD0; -.
PDBsum; 2WDQ; -.
PDBsum; 2WDR; -.
PDBsum; 2WDV; -.
PDBsum; 2WP9; -.
PDBsum; 2WS3; -.
PDBsum; 2WU2; -.
PDBsum; 2WU5; -.
ProteinModelPortal; P07014; -.
SMR; P07014; -.
BioGrid; 4261950; 32.
BioGrid; 849677; 1.
ComplexPortal; CPX-1931; Respiratory chain complex II.
DIP; DIP-10836N; -.
IntAct; P07014; 8.
STRING; 316385.ECDH10B_0791; -.
DrugBank; DB04631; Atpenin A5.
DrugBank; DB08690; UBIQUINONE-2.
EPD; P07014; -.
PaxDb; P07014; -.
PRIDE; P07014; -.
EnsemblBacteria; AAC73818; AAC73818; b0724.
EnsemblBacteria; BAA35391; BAA35391; BAA35391.
GeneID; 945300; -.
KEGG; ecj:JW0714; -.
KEGG; eco:b0724; -.
PATRIC; fig|1411691.4.peg.1548; -.
EchoBASE; EB0925; -.
EcoGene; EG10932; sdhB.
eggNOG; ENOG4105E33; Bacteria.
eggNOG; COG0479; LUCA.
HOGENOM; HOG000160590; -.
InParanoid; P07014; -.
KO; K00240; -.
PhylomeDB; P07014; -.
BioCyc; EcoCyc:SDH-FE-S; -.
BioCyc; MetaCyc:SDH-FE-S; -.
UniPathway; UPA00223; UER01005.
EvolutionaryTrace; P07014; -.
PRO; PR:P07014; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IMP:EcoCyc.
GO; GO:0051538; F:3 iron, 4 sulfur cluster binding; IDA:EcoCyc.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IMP:EcoCyc.
GO; GO:0009055; F:electron transfer activity; IMP:EcoCyc.
GO; GO:0051536; F:iron-sulfur cluster binding; IDA:EcoCyc.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008177; F:succinate dehydrogenase (ubiquinone) activity; IEA:UniProtKB-EC.
GO; GO:0009060; P:aerobic respiration; IEP:EcoCyc.
GO; GO:0022904; P:respiratory electron transport chain; IBA:GO_Central.
GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-UniPathway.
CDD; cd00207; fer2; 1.
Gene3D; 1.10.1060.10; -; 1.
Gene3D; 3.10.20.30; -; 1.
InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
InterPro; IPR017896; 4Fe4S_Fe-S-bd.
InterPro; IPR017900; 4Fe4S_Fe_S_CS.
InterPro; IPR012675; Beta-grasp_dom_sf.
InterPro; IPR009051; Helical_ferredxn.
InterPro; IPR004489; Succ_DH/fum_Rdtase_Fe-S.
InterPro; IPR025192; Succ_DH/fum_Rdtase_N.
Pfam; PF13085; Fer2_3; 1.
SUPFAM; SSF46548; SSF46548; 1.
SUPFAM; SSF54292; SSF54292; 1.
TIGRFAMs; TIGR00384; dhsB; 1.
PROSITE; PS51085; 2FE2S_FER_2; 1.
PROSITE; PS00198; 4FE4S_FER_1; 1.
PROSITE; PS51379; 4FE4S_FER_2; 1.
1: Evidence at protein level;
2Fe-2S; 3D-structure; 3Fe-4S; 4Fe-4S; Cell inner membrane;
Cell membrane; Complete proteome; Direct protein sequencing;
Electron transport; Iron; Iron-sulfur; Membrane; Metal-binding;
Oxidoreductase; Reference proteome; Transport;
Tricarboxylic acid cycle.
CHAIN 1 238 Succinate dehydrogenase iron-sulfur
subunit.
/FTId=PRO_0000158688.
DOMAIN 8 97 2Fe-2S ferredoxin-type.
{ECO:0000255|PROSITE-ProRule:PRU00465}.
DOMAIN 139 169 4Fe-4S ferredoxin-type.
{ECO:0000255|PROSITE-ProRule:PRU00711}.
METAL 55 55 Iron-sulfur 1 (2Fe-2S).
METAL 60 60 Iron-sulfur 1 (2Fe-2S).
METAL 75 75 Iron-sulfur 1 (2Fe-2S).
METAL 149 149 Iron-sulfur 2 (4Fe-4S).
METAL 152 152 Iron-sulfur 2 (4Fe-4S).
METAL 155 155 Iron-sulfur 2 (4Fe-4S).
METAL 159 159 Iron-sulfur 3 (3Fe-4S).
METAL 206 206 Iron-sulfur 3 (3Fe-4S).
METAL 212 212 Iron-sulfur 3 (3Fe-4S).
METAL 216 216 Iron-sulfur 2 (4Fe-4S).
BINDING 164 164 Ubiquinone; shared with SdhD subunit.
{ECO:0000269|PubMed:12560550}.
STRAND 2 9 {ECO:0000244|PDB:2WDQ}.
TURN 12 14 {ECO:0000244|PDB:2WDQ}.
STRAND 19 26 {ECO:0000244|PDB:2WDQ}.
STRAND 29 31 {ECO:0000244|PDB:1NEK}.
HELIX 35 45 {ECO:0000244|PDB:2WDQ}.
STRAND 54 60 {ECO:0000244|PDB:2WDQ}.
STRAND 64 67 {ECO:0000244|PDB:2WDQ}.
STRAND 70 73 {ECO:0000244|PDB:2WDQ}.
HELIX 74 76 {ECO:0000244|PDB:2WDQ}.
HELIX 79 81 {ECO:0000244|PDB:2WDQ}.
STRAND 89 92 {ECO:0000244|PDB:2WDQ}.
STRAND 97 101 {ECO:0000244|PDB:2WDQ}.
STRAND 103 105 {ECO:0000244|PDB:2ACZ}.
HELIX 108 116 {ECO:0000244|PDB:2WDQ}.
STRAND 130 132 {ECO:0000244|PDB:2WDQ}.
HELIX 137 141 {ECO:0000244|PDB:2WDQ}.
TURN 142 148 {ECO:0000244|PDB:2WDQ}.
HELIX 156 158 {ECO:0000244|PDB:2WDQ}.
HELIX 160 164 {ECO:0000244|PDB:2WDQ}.
TURN 166 168 {ECO:0000244|PDB:2WDQ}.
HELIX 172 182 {ECO:0000244|PDB:2WDQ}.
HELIX 190 195 {ECO:0000244|PDB:2WDQ}.
TURN 200 205 {ECO:0000244|PDB:2WDQ}.
HELIX 211 215 {ECO:0000244|PDB:2WDQ}.
HELIX 222 237 {ECO:0000244|PDB:2WDQ}.
SEQUENCE 238 AA; 26770 MW; 226F60C55F5AC35A CRC64;
MRLEFSIYRY NPDVDDAPRM QDYTLEADEG RDMMLLDALI QLKEKDPSLS FRRSCREGVC
GSDGLNMNGK NGLACITPIS ALNQPGKKIV IRPLPGLPVI RDLVVDMGQF YAQYEKIKPY
LLNNGQNPPA REHLQMPEQR EKLDGLYECI LCACCSTSCP SFWWNPDKFI GPAGLLAAYR
FLIDSRDTET DSRLDGLSDA FSVFRCHSIM NCVSVCPKGL NPTRAIGHIK SMLLQRNA


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