P0AGE9 (SUCD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Succinyl-CoA ligase [ADP-forming] subunit alpha
EC=6.2.1.5

Alternative name(s):
Succinyl-CoA synthetase subunit alpha
Short name=SCS-alpha

Gene names

Name:	sucD
Ordered Locus Names:	b0729, JW0718

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	289 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)

Catalytic activity	ATP + succinate + CoA = ADP + phosphate + succinyl-CoA.
Enzyme regulation	Exhibits two interesting properties: "substrate synergism", in which the enzyme is most active for the catalysis of its partial reactions only when all the substrate binding sites are occupied, and "catalytic cooperativity" between alternating active sites in the tetramer, whereby the interaction of substrates (particularly ATP) at one site is needed to promote catalysis at the other.
Subunit structure	Heterotetramer of two alpha and two beta subunits.
Miscellaneous	Succinyl-CoA synthetase (SCS) of E.coli catalyzes its reaction via three steps that involve phosphoryl enzyme and enzyme-bound succinyl phosphate as intermediates. During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact. The succinyl-CoA synthetases of eukaryotes and Gram-positive bacteria differ from the Gram-negative enzymes in containing single alpha-beta dimers.
Sequence similarities	Belongs to the succinate/malate CoA ligase alpha subunit family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	tricarboxylic acid cycle Inferred from direct assay. Source: EcoliWiki
Cellular component	cytoplasm Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP citrate synthase activity Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct succinate-CoA ligase (ADP-forming) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
sucC	P0A836	3	EBI-369078,EBI-369117

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6 Ref.7 Ref.8

Chain

2 – 289

288

Succinyl-CoA ligase [ADP-forming] subunit alpha

PRO_0000102791

Sites

Active site

247

1

Tele-phosphohistidine intermediate

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

289

Helix Strand Turn

Details...

Beta strand

10 – 14

5

Turn

15 – 17

3

Helix

19 – 31

13

Beta strand

34 – 39

6

Beta strand

51 – 56

6

Helix

57 – 64

8

Beta strand

68 – 71

4

Helix

75 – 77

3

Helix

78 – 87

10

Beta strand

91 – 95

5

Helix

102 – 115

14

Beta strand

118 – 120

3

Beta strand

122 – 124

3

Beta strand

126 – 129

4

Turn

130 – 132

3

Beta strand

133 – 138

6

Beta strand

147 – 153

7

Helix

155 – 167

13

Beta strand

172 – 177

6

Beta strand

180 – 183

4

Helix

188 – 196

9

Beta strand

203 – 213

11

Helix

214 – 225

12

Beta strand

230 – 235

6

Helix

259 – 268

10

Helix

277 – 279

3

Helix

280 – 287

8

Sequences

	Sequence		Length	Mass (Da)
	P0AGE9 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 8AC27AD828BC51B3	FASTA	289	29,777
	10 20 30 40 50 60 MSILIDKNTK VICQGFTGSQ GTFHSEQAIA YGTKMVGGVT PGKGGTTHLG LPVFNTVREA 70 80 90 100 110 120 VAATGATASV IYVPAPFCKD SILEAIDAGI KLIITITEGI PTLDMLTVKV KLDEAGVRMI 130 140 150 160 170 180 GPNCPGVITP GECKIGIQPG HIHKPGKVGI VSRSGTLTYE AVKQTTDYGF GQSTCVGIGG 190 200 210 220 230 240 DPIPGSNFID ILEMFEKDPQ TEAIVMIGEI GGSAEEEAAA YIKEHVTKPV VGYIAGVTAP 250 260 270 280 KGKRMGHAGA IIAGGKGTAD EKFAALEAAG VKTVRSLADI GEALKTVLK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Primary structure of the succinyl-CoA synthetase of Escherichia coli." Buck D., Spencer M.E., Guest J.R. Biochemistry 24:6245-6252(1985) [PubMed: 3002435] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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: 8905232] [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: 9278503] [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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon." Buck D., Guest J.R. Biochem. J. 260:737-747(1989) [PubMed: 2548486] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 173-289.
[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: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-20. Strain: K12 / EMG2.
[7]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-12. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Identification of phosphoproteins in Escherichia coli." Freestone P., Grant S., Toth I., Norris V. Mol. Microbiol. 15:573-580(1995) [PubMed: 7783627] [Abstract] Cited for: PHOSPHORYLATION, PROTEIN SEQUENCE OF 2-11.
[9]	"The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-A resolution." Wolodko W.T., Fraser M.E., James M.N.G., Bridger W.A. J. Biol. Chem. 269:10883-10890(1994) [PubMed: 8144675] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[10]	"A detailed structural description of Escherichia coli succinyl-CoA synthetase." Fraser M.E., James M.N., Bridger W.A., Wolodko W.T. J. Mol. Biol. 285:1633-1653(1999) [PubMed: 9917402] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[11]	"ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by X-ray crystallography." Joyce M.A., Fraser M.E., James M.N., Bridger W.A., Wolodko W.T. Biochemistry 39:17-25(2000) [PubMed: 10625475] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01619 Genomic DNA. Translation: AAA23900.1.
U00096 Genomic DNA. Translation: AAC73823.1.
AP009048 Genomic DNA. Translation: BAA35395.1.
X15790 Genomic DNA. Translation: CAA33792.1.

PIR

SYECSA. A90499.

RefSeq

NP_415257.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CQI	X-ray	3.30	A/D	2-287	[»]
1CQJ	X-ray	2.90	A/D	2-287	[»]
1JKJ	X-ray	2.35	A/D	2-289	[»]
1JLL	X-ray	2.69	A/D	2-289	[»]
1SCU	X-ray	2.50	A/D	2-289	[»]
2NU6	X-ray	2.55	A/D	2-288	[»]
2NU7	X-ray	2.20	A/D	2-288	[»]
2NU8	X-ray	2.15	A/D	2-288	[»]
2NU9	X-ray	2.90	A/D/F/H	2-289	[»]
2NUA	X-ray	2.95	A/D	2-288	[»]
2SCU	X-ray	2.30	A/D	2-289	[»]

ProteinModelPortal

P0AGE9.

SMR

P0AGE9. Positions 2-288.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31851N.

IntAct

P0AGE9. 7 interactions.

MINT

MINT-1219451.

2D gel databases

SWISS-2DPAGE

P0AGE9.

ECO2DBASE

H028.0. 6TH EDITION.

Proteomic databases

PRIDE

P0AGE9.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000004064; EBESCP00000004064; EBESCG00000003319.
EBESCT00000004065; EBESCP00000004065; EBESCG00000003319.
EBESCT00000014676; EBESCP00000013967; EBESCG00000013737.

GeneID

945314.

GenomeReviews

Gene locus JW0718 in contig AP009048_GR.
Gene locus b0729 in contig U00096_GR.

KEGG

ecj:JW0718.
eco:b0729.

PATRIC

32116653. VBIEscCol129921_0759.

Organism-specific databases

EchoBASE

EB0975.

EcoGene

EG10982. sucD.

Phylogenomic databases

eggNOG

COG0074.

GeneTree

EBGT00050000010106.

HOGENOM

HBG615372.

OMA

DETTEAI.

PhylomeDB

P0AGE9.

ProtClustDB

PRK05678.

Enzyme and pathway databases

BioCyc

EcoCyc:SUCCCOASYN-ALPHA.
MetaCyc:SUCCCOASYN-ALPHA.

Gene expression databases

Genevestigator

P0AGE9.

Family and domain databases

InterPro

IPR017440. Cit_synth/succinyl-CoA_lig_AS.
IPR003781. CoA-bd.
IPR005810. CoA_lig_alpha.
IPR005811. CoA_ligase.
IPR016040. NAD(P)-bd_dom.
IPR016102. Succinyl-CoA_synth-like.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
G3DSA:3.40.50.261. Succinyl-CoA_synth-like. 1 hit.

KO

K01902.

Pfam

PF02629. CoA_binding. 1 hit.
PF00549. Ligase_CoA. 1 hit.
[Graphical view]

PIRSF

PIRSF001553. SucCS_alpha. 1 hit.

PRINTS

PR01798. SCOASYNTHASE.

SMART

SM00881. CoA_binding. 1 hit.
[Graphical view]

SUPFAM

SSF52210. CoA_ligase. 1 hit.

TIGRFAMs

TIGR01019. SucCoAalpha. 1 hit.

PROSITE

PS01216. SUCCINYL_COA_LIG_1. 1 hit.
PS00399. SUCCINYL_COA_LIG_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SUCD_ECOLI

Accession

Primary (citable) accession number: P0AGE9
Secondary accession number(s): P07459

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 60 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program