Reviewed, UniProtKB/Swiss-Prot P21801 (DHSB_YEAST)

Names and origin

Protein names

Recommended name:
    Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
    EC=1.3.5.1
Alternative name(s):
    Iron-sulfur subunit of complex II
      Short name=Ip

Gene names

Name:	SDH2
Synonyms:	SDH, SDHB
Ordered Locus Names:	YLL041C

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	266 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH1 and SDH2 form the catalytic dimer. Electrons flow from succinate to the FAD bound to SDH1, and sequentially through the iron-sulfur clusters bound to SDH2 and enter the membrane dimer formed by SDH3 and SDH4.
Catalytic activity	Succinate + ubiquinone = fumarate + ubiquinol.
Cofactor	Binds 1 2Fe-2S cluster By similarity. Binds 1 3Fe-4S cluster By similarity. Binds 1 4Fe-4S cluster By similarity.
Pathway	Carbohydrate metabolism; tricarboxylic acid cycle; fumarate from succinate (eukaryal route): step 1/1.
Subunit structure	Component of complex II composed of four subunits: a flavoprotein (FP), an iron-sulfur protein (IP), and a cytochrome b composed of a large and a small subunit By similarity.
Subcellular location	Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.
Miscellaneous	Present with 9540 molecules/cell in log phase SD medium. Ref.8
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	Membrane Mitochondrion Mitochondrion inner membrane
Domain	Transit peptide
Ligand	2Fe-2S 3Fe-4S 4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	mitochondrial electron transport, succinate to ubiquinone Traceable author statement. Source: SGD transport Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Inferred from mutant phenotype. Source: SGD
Cellular component	extrinsic to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrial respiratory chain complex II Inferred from direct assay. Source: SGD
Molecular function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 3 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct succinate dehydrogenase (ubiquinone) activity Inferred from direct assay. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SDH1	Q00711	1	EBI-5856,EBI-5851

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – ?20

20

Mitochondrion

Chain

?21 – 266

246

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

PRO_0000010353

Regions

Domain

36 – 127

92

2Fe-2S ferredoxin-type

Domain

169 – 199

31

4Fe-4S ferredoxin-type

Sites

Metal binding

87

1

Iron-sulfur 1 (2Fe-2S) By similarity

Metal binding

92

1

Iron-sulfur 1 (2Fe-2S) By similarity

Metal binding

95

1

Iron-sulfur 1 (2Fe-2S) By similarity

Metal binding

107

1

Iron-sulfur 1 (2Fe-2S) By similarity

Metal binding

179

1

Iron-sulfur 2 (4Fe-4S) By similarity

Metal binding

182

1

Iron-sulfur 2 (4Fe-4S) By similarity

Metal binding

185

1

Iron-sulfur 2 (4Fe-4S) By similarity

Metal binding

189

1

Iron-sulfur 3 (3Fe-4S) By similarity

Metal binding

236

1

Iron-sulfur 3 (3Fe-4S) By similarity

Metal binding

242

1

Iron-sulfur 3 (3Fe-4S) By similarity

Metal binding

246

1

Iron-sulfur 2 (4Fe-4S) By similarity

Binding site

194

1

Ubiquinone; shared with DHSD By similarity

Experimental info

Mutagenesis

260 – 266

7

Missing: Abolishes SDH activity and complex assembly. Ref.6

Mutagenesis

260

1

K → T: Abolishes SDH activity. No effect on complex assembly and stability; when associated with T-261. Ref.6

Mutagenesis

261

1

K → T: Abolishes SDH activity. No effect on complex assembly and stability; when associated with T-260. Ref.6

Secondary structure

1

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266

Helix Strand Turn

Details...

Beta strand

32 – 39

8

Beta strand

43 – 45

3

Beta strand

47 – 49

3

Beta strand

52 – 58

7

Helix

66 – 75

10

Beta strand

87 – 90

4

Beta strand

96 – 102

7

Turn

106 – 108

3

Beta strand

120 – 122

3

Beta strand

125 – 131

7

Helix

138 – 146

9

Beta strand

160 – 162

3

Helix

167 – 171

5

Turn

172 – 178

7

Helix

184 – 187

4

Helix

190 – 194

5

Turn

195 – 198

4

Helix

202 – 213

12

Helix

220 – 227

8

Turn

230 – 235

6

Helix

241 – 245

5

Helix

252 – 265

14

Sequences

	Sequence		Length	Mass (Da)
	P21801-1 [UniParc]. Last modified May 1, 1991. Version 1. Checksum: C14170F3670F6930	FASTA	266	30,231
	10 20 30 40 50 60 MLNVLLRRKA FCLVTKKGMA TATTAAATHT PRLKTFKVYR WNPDEPSAKP HLQSYQVDLN 70 80 90 100 110 120 DCGPMVLDAL LKIKDEQDST LTFRRSCREG ICGSCAMNIG GRNTLACICK IDQNESKQLK 130 140 150 160 170 180 IYPLPHMFIV KDLVPDLTNF YQQYKSIQPY LQRSSFPKDG TEVLQSIEDR KKLDGLYECI 190 200 210 220 230 240 LCACCSTSCP SYWWNQEQYL GPAVLMQAYR WLIDSRDQAT KTRKAMLNNS MSLYRCHTIM 250 260 NCTRTCPKGL NPGLAIAEIK KSLAFA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of the iron-sulfur subunit gene of succinate dehydrogenase from Saccharomyces cerevisiae." Lombardo A., Carine K., Scheffler I.E. J. Biol. Chem. 265:10419-10423(1990) [PubMed: 2191948] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed: 9169871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"Use of the DNA polymerase chain reaction for homology probing: isolation of partial cDNA or genomic clones encoding the iron-sulfur protein of succinate dehydrogenase from several species." Gould S.J., Subramani S., Scheffler I.E. Proc. Natl. Acad. Sci. U.S.A. 86:1934-1938(1989) [PubMed: 2494655] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 101-242.
[5]	Erratum Gould S.J., Subramani S., Scheffler I.E. Proc. Natl. Acad. Sci. U.S.A. 90:2556-2556(1993)
[6]	"The C-terminus of the succinate dehydrogenase IP peptide of Saccharomyces cerevisiae is significant for assembly of complex II." Schmidt D.M., Saghbini M., Scheffler I.E. Biochemistry 31:8442-8448(1992) [PubMed: 1390628] [Abstract] Cited for: MUTAGENESIS OF LYS-260; LYS-261 AND 260-LYS--ALA-266.
[7]	"The Saccharomyces cerevisiae mitochondrial succinate:ubiquinone oxidoreductase." Lemire B.D., Oyedotun K.S. Biochim. Biophys. Acta 1553:102-116(2002) [PubMed: 11803020] [Abstract] Cited for: REVIEW ON SUCCINATE DEHYDROGENASE.
[8]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"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: 14672929] [Abstract] Cited for: 3D-STRUCTURE MODELING OF 21-266.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J05487 Genomic DNA. Translation: AAA35021.1.
Z73146 Genomic DNA. Translation: CAA97492.1.
AY558189 Genomic DNA. Translation: AAS56515.1.

PIR

RDBYIS. A35435.

RefSeq

NP_013059.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ORZ	model	-	B	21-266	[»]
1PB4	model	-	B	21-266	[»]

SMR

P21801. Positions 30-264.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5856N.

IntAct

P21801. 3 interactions.

STRING

P21801.

Proteomic databases

PeptideAtlas

P21801.

PRIDE

P21801.

Genome annotation databases

Ensembl

YLL041C; YLL041C; YLL041C; Saccharomyces cerevisiae. [Genome view]

GeneID

850685.

KEGG

sce:YLL041C.

NMPDR

fig|4932.3.peg.4050.

Organism-specific databases

CYGD

YLL041c.

SGD

S000003964. SDH2.

Phylogenomic databases

eggNOG

fuNOG06803.

HOGENOM

HBG616382.

OMA

SLIAERH.

OrthoDB

EOG9BZPK2.

PhylomeDB

P21801.

Enzyme and pathway databases

BRENDA

1.3.5.1. 250.

Gene expression databases

ArrayExpress

P21801.

Genevestigator

P21801.

GermOnline

YLL041C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR006058. 2Fe2S_fd_BS.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR012675. b-grasp_ferredoxin-like.
IPR001041. Ferredoxin.
IPR012285. Fum_reductase_C.
IPR009051. Helical_ferredxn.
IPR004489. Succ_DH/fum_Rdtase_Fe-S.
[Graphical view]

Gene3D

G3DSA:3.10.20.30. Ferredoxin_fold. 1 hit.
G3DSA:1.10.1060.10. Fum_reductase_C. 1 hit.

Pfam

PF00111. Fer2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00384. dhsB. 1 hit.

PROSITE

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

ProtoNet

Search...

Other Resources

NextBio

966692.

Entry information

Entry name

DHSB_YEAST

Accession

Primary (citable) accession number: P21801

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	May 1, 1991
Last modified:	February 9, 2010
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)