P07014 (DHSB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Succinate dehydrogenase iron-sulfur subunit
EC=1.3.99.1

Gene names

Name:	sdhB
Ordered Locus Names:	b0724, JW0714

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	238 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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	Succinate + acceptor = fumarate + reduced acceptor.
Cofactor	Binds 1 2Fe-2S cluster. Ref.8 Ref.9 Ref.10 Binds 1 3Fe-4S cluster. Ref.8 Ref.9 Ref.10 Binds 1 4Fe-4S cluster. Ref.8 Ref.9 Ref.10
Pathway	Carbohydrate metabolism; tricarboxylic acid cycle; fumarate from succinate (bacterial route): step 1/1.
Subunit structure	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. Ref.7 Ref.8 Ref.9 Ref.10
Subcellular location	Cell inner membrane; Peripheral membrane protein Ref.7.
Sequence similarities	Belongs to the succinate dehydrogenase/fumarate reductase iron-sulfur protein family. Contains 1 2Fe-2S ferredoxin-type domain. Contains 1 4Fe-4S ferredoxin-type domain.

Ontologies

Keywords
Biological process	Electron transport Transport Tricarboxylic acid cycle
Cellular component	Cell inner membrane Cell membrane Membrane
Ligand	2Fe-2S 3Fe-4S 4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	aerobic respiration Inferred from expression pattern PubMed 7783618. Source: EcoCyc electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from mutant phenotype PubMed 1312028. Source: EcoCyc 3 iron, 4 sulfur cluster binding Inferred from direct assay PubMed 2987254. Source: EcoCyc 4 iron, 4 sulfur cluster binding Inferred from mutant phenotype PubMed 3008846. Source: EcoCyc electron carrier activity Inferred from mutant phenotype PubMed 16864590. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW succinate dehydrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
sdhA	P0AC41	5	EBI-1035514,EBI-371263

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 238

238

Succinate dehydrogenase iron-sulfur subunit

PRO_0000158688

Regions

Domain

8 – 97

90

2Fe-2S ferredoxin-type

Domain

139 – 169

31

4Fe-4S ferredoxin-type

Sites

Metal binding

55

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

60

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

75

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

149

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

152

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

155

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

159

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

206

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

212

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

216

1

Iron-sulfur 2 (4Fe-4S)

Binding site

164

1

Ubiquinone; shared with SdhD subunit

Secondary structure

1

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238

Helix Strand Turn

Details...

Beta strand

2 – 9

8

Turn

12 – 14

3

Beta strand

19 – 26

8

Beta strand

29 – 31

3

Helix

35 – 45

11

Beta strand

54 – 60

7

Beta strand

64 – 67

4

Beta strand

70 – 73

4

Helix

74 – 76

3

Helix

79 – 81

3

Beta strand

89 – 92

4

Beta strand

97 – 101

5

Beta strand

103 – 105

3

Helix

108 – 116

9

Beta strand

130 – 132

3

Helix

137 – 141

5

Turn

142 – 148

7

Helix

156 – 158

3

Helix

160 – 164

5

Turn

166 – 168

3

Helix

172 – 182

11

Helix

190 – 195

6

Turn

200 – 205

6

Helix

211 – 215

5

Helix

222 – 237

16

Sequences

	Sequence		Length	Mass (Da)
	P07014 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: 226F60C55F5AC35A	FASTA	238	26,770
	10 20 30 40 50 60 MRLEFSIYRY NPDVDDAPRM QDYTLEADEG RDMMLLDALI QLKEKDPSLS FRRSCREGVC 70 80 90 100 110 120 GSDGLNMNGK NGLACITPIS ALNQPGKKIV IRPLPGLPVI RDLVVDMGQF YAQYEKIKPY 130 140 150 160 170 180 LLNNGQNPPA REHLQMPEQR EKLDGLYECI LCACCSTSCP SFWWNPDKFI GPAGLLAAYR 190 200 210 220 230 FLIDSRDTET DSRLDGLSDA FSVFRCHSIM NCVSVCPKGL NPTRAIGHIK SMLLQRNA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence encoding the iron-sulphur protein subunit of the succinate dehydrogenase of Escherichia coli." Darlison M.G., Guest J.R. Biochem. J. 223:507-517(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"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." 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. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate dehydrogenase of Escherichia coli K12." Darlison M.G., Spencer M.E., Guest J.R. Eur. J. Biochem. 141:351-359(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 231-238.
[6]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-11. Strain: K12 / EMG2.
[7]	"Protein complexes of the Escherichia coli cell envelope." Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L., von Heijne G., Daley D.O. J. Biol. Chem. 280:34409-34419(2005) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, SUBCELLULAR LOCATION. Strain: BL21-DE3.
[8]	"Architecture of succinate dehydrogenase and reactive oxygen species generation." Yankovskaya V., Horsefield R., Toernroth S., Luna-Chavez C., Miyoshi H., Leger C., Byrne B., Cecchini G., Iwata S. Science 299:700-704(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR CLUSTERS AND UBIQUINONE, COFACTOR, SUBUNIT.
[9]	"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." Horsefield R., Yankovskaya V., Sexton G., Whittingham W., Shiomi K., Omura S., Byrne B., Cecchini G., Iwata S. J. Biol. Chem. 281:7309-7316(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR CLUSTERS, COFACTOR, SUBUNIT.
[10]	"Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site." Ruprecht J., Yankovskaya V., Maklashina E., Iwata S., Cecchini G. J. Biol. Chem. 284:29836-29846(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR CLUSTERS, COFACTOR, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01619 Genomic DNA. Translation: AAA23896.1.
X01070 Genomic DNA. Translation: CAA25534.1.
U00096 Genomic DNA. Translation: AAC73818.1.
AP009048 Genomic DNA. Translation: BAA35391.1.
X00661 Genomic DNA. Translation: CAA25279.1.

PIR

DEECSI. A28837.

RefSeq

NP_415252.1. NC_000913.2.
YP_489004.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NEK	X-ray	2.60	B	1-238	[»]
1NEN	X-ray	2.90	B	1-238	[»]
2ACZ	X-ray	3.10	B	1-238	[»]
2AD0	model	-	B	1-238	[»]
2WDQ	X-ray	2.40	B/F/J	1-238	[»]
2WDR	X-ray	3.20	B/F/J	1-238	[»]
2WDV	X-ray	3.20	B/F/J	1-238	[»]
2WP9	X-ray	2.70	B/F/J	1-238	[»]
2WS3	X-ray	3.20	B/F/J	1-238	[»]
2WU2	X-ray	2.50	B/F/J	1-238	[»]
2WU5	X-ray	2.80	B/F/J	1-238	[»]

ProteinModelPortal

P07014.

SMR

P07014. Positions 1-238.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10836N.

IntAct

P07014. 4 interactions.

STRING

511145.b0724.

Proteomic databases

PaxDb

P07014.

PRIDE

P07014.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73818; AAC73818; b0724.
BAA35391; BAA35391; BAA35391.

GeneID

12932956.
945300.

KEGG

ecj:Y75_p0704.
eco:b0724.

PATRIC

32116643. VBIEscCol129921_0754.

Organism-specific databases

EchoBASE

EB0925.

EcoGene

EG10932. sdhB.

Phylogenomic databases

eggNOG

COG0479.

HOGENOM

HOG000160590.

KO

K00240.

OMA

NCSRTCP.

ProtClustDB

PRK05950.

Enzyme and pathway databases

BioCyc

EcoCyc:SDH-FE-S.
ECOL316407:JW0714-MONOMER.

UniPathway

UPA00223; UER01005.

Gene expression databases

Genevestigator

P07014.

Family and domain databases

Gene3D

1.10.1060.10. 1 hit.
3.10.20.30. 1 hit.

InterPro

IPR001041. 2Fe-2S_ferredoxin-type.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR012675. Beta-grasp_dom.
IPR012285. Fum_reductase_C.
IPR009051. Helical_ferredxn.
IPR004489. Succ_DH/fum_Rdtase_Fe-S.
IPR025192. Succ_DH/fum_Rdtase_N.
[Graphical view]

Pfam

PF13085. Fer2_3. 1 hit.
[Graphical view]

SUPFAM

SSF54292. Ferredoxin. 1 hit.
SSF46548. Helical_ferredxn. 1 hit.

TIGRFAMs

TIGR00384. dhsB. 1 hit.

PROSITE

PS00197. 2FE2S_FER_1. False negative.
PS51085. 2FE2S_FER_2. 1 hit.
PS00198. 4FE4S_FER_1. 1 hit.
PS51379. 4FE4S_FER_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P07014.

Entry information

Entry name

DHSB_ECOLI

Accession

Primary (citable) accession number: P07014

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	May 29, 2013
This is version 136 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program