P0AFG6 (ODO2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
EC=2.3.1.61

Alternative name(s):
2-oxoglutarate dehydrogenase complex component E2
Short name=OGDC-E2
Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex

Gene names

Name:	sucB
Ordered Locus Names:	b0727, JW0716

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	405 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	The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO2. It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).
Catalytic activity	Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.
Cofactor	Binds 1 lipoyl cofactor covalently.
Pathway	Amino-acid degradation; L-lysine degradation via saccharopine pathway; glutaryl-CoA from L-lysine: step 6/6.
Subunit structure	Forms a 24-polypeptide structural core with octahedral symmetry.
Sequence similarities	Belongs to the 2-oxoacid dehydrogenase family. Contains 1 lipoyl-binding domain.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Domain	Lipoyl
Molecular function	Acyltransferase Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	tricarboxylic acid cycle Inferred from mutant phenotype. Source: EcoliWiki
Cellular component	oxoglutarate dehydrogenase complex Inferred from direct assay. Source: EcoliWiki
Molecular function	dihydrolipoyllysine-residue succinyltransferase activity Inferred from direct assay. Source: EcoliWiki lipoic acid binding Inferred from direct assay. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6

Chain

2 – 405

404

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

PRO_0000162262

Regions

Domain

2 – 77

76

Lipoyl-binding

Sites

Active site

376

1

Active site

380

1

Amino acid modifications

Modified residue

44

1

N6-lipoyllysine

Modified residue

148

1

N6-acetyllysine Ref.7

Secondary structure

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405

Helix Strand Turn

Details...

Helix

118 – 124

7

Helix

129 – 131

3

Helix

143 – 149

7

Beta strand

175 – 180

6

Helix

183 – 196

14

Beta strand

201 – 209

9

Helix

211 – 228

18

Helix

235 – 248

14

Turn

250 – 253

4

Beta strand

255 – 257

3

Beta strand

260 – 266

7

Beta strand

269 – 271

3

Beta strand

273 – 275

3

Beta strand

278 – 280

3

Helix

287 – 289

3

Helix

292 – 305

14

Turn

306 – 309

4

Helix

313 – 316

4

Beta strand

320 – 325

6

Helix

326 – 329

4

Beta strand

343 – 358

16

Beta strand

361 – 375

15

Turn

376 – 378

3

Helix

381 – 396

16

Helix

400 – 403

4

Sequences

	Sequence		Length	Mass (Da)
	P0AFG6 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 8439E48C6D381277	FASTA	405	44,011
	10 20 30 40 50 60 MSSVDILVPD LPESVADATV ATWHKKPGDA VVRDEVLVEI ETDKVVLEVP ASADGILDAV 70 80 90 100 110 120 LEDEGTTVTS RQILGRLREG NSAGKETSAK SEEKASTPAQ RQQASLEEQN NDALSPAIRR 130 140 150 160 170 180 LLAEHNLDAS AIKGTGVGGR LTREDVEKHL AKAPAKESAP AAAAPAAQPA LAARSEKRVP 190 200 210 220 230 240 MTRLRKRVAE RLLEAKNSTA MLTTFNEVNM KPIMDLRKQY GEAFEKRHGI RLGFMSFYVK 250 260 270 280 290 300 AVVEALKRYP EVNASIDGDD VVYHNYFDVS MAVSTPRGLV TPVLRDVDTL GMADIEKKIK 310 320 330 340 350 360 ELAVKGRDGK LTVEDLTGGN FTITNGGVFG SLMSTPIINP PQSAILGMHA IKDRPMAVNG 370 380 390 400 QVEILPMMYL ALSYDHRLID GRESVGFLVT IKELLEDPTR LLLDV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the sucB gene encoding the dihydrolipoamide succinyltransferase of Escherichia coli K12 and homology with the corresponding acetyltransferase." Spencer M.E., Darlison M.G., Stephens P.E., Duckenfield I.K., Guest J.R. Eur. J. Biochem. 141:361-374(1984) [PubMed: 6376124] [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: 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]	"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: 6376123] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-12.
[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 2-13. Strain: K12 / EMG2.
[7]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-148, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[8]	"Three-dimensional structure of the lipoyl domain from the dihydrolipoyl succinyltransferase component of the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli." Ricaud P.M., Howard M.J., Roberts E.L., Broadhurst R.W., Perham R.N. J. Mol. Biol. 264:179-190(1996) [PubMed: 8950276] [Abstract] Cited for: STRUCTURE BY NMR OF 1-81.
[9]	"Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli." Robien M.A., Clore G.M., Omichinski J.G., Perham R.N., Appella E., Sakaguchi K., Gronenborn A.M. Biochemistry 31:3463-3471(1992) [PubMed: 1554728] [Abstract] Cited for: STRUCTURE BY NMR OF 104-153.
[10]	"Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex." Knapp J.E., Mitchell D.T., Yazdi M.A., Ernst S.R., Reed L.J., Hackert M.L. J. Mol. Biol. 280:655-668(1998) [PubMed: 9677295] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405.
[11]	"Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase." Knapp J.E., Carroll D., Lawson J.E., Ernst S.R., Reed L.J., Hackert M.L. Protein Sci. 9:37-48(2000) [PubMed: 10739245] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01619 Genomic DNA. Translation: AAA23898.1.
X00664 Genomic DNA. Translation: CAA25284.1.
U00096 Genomic DNA. Translation: AAC73821.1.
AP009048 Genomic DNA. Translation: BAA35393.1.
X00661 Genomic DNA. Translation: CAA25281.1.

PIR

XUECSD. F64808.

RefSeq

NP_415255.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BAL	NMR	-	A	104-153	[»]
1BBL	NMR	-	A	104-153	[»]
1C4T	X-ray	3.00	A/B/C	173-405	[»]
1E2O	X-ray	3.00	A	173-405	[»]
1PMR	NMR	-	A	2-81	[»]
1SCZ	X-ray	2.20	A	173-405	[»]
1W4H	NMR	-	A	109-153	[»]
2BTG	NMR	-	A	109-153	[»]
2BTH	NMR	-	A	109-153	[»]
2WXC	NMR	-	A	109-153	[»]

ProteinModelPortal

P0AFG6.

SMR

P0AFG6. Positions 2-81, 104-153, 173-405.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35787N.

IntAct

P0AFG6. 39 interactions.

MINT

MINT-1242608.

2D gel databases

SWISS-2DPAGE

P0AFG6.

ECO2DBASE

F050.3. 6TH EDITION.

Proteomic databases

PRIDE

P0AFG6.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001770; EBESCP00000001770; EBESCG00000001459.
EBESCT00000001771; EBESCP00000001771; EBESCG00000001459.
EBESCT00000017897; EBESCP00000017188; EBESCG00000016953.

GeneID

945307.

GenomeReviews

Gene locus JW0716 in contig AP009048_GR.
Gene locus b0727 in contig U00096_GR.

KEGG

ecj:JW0716.
eco:b0727.

PATRIC

32116649. VBIEscCol129921_0757.

Organism-specific databases

EchoBASE

EB0973.

EcoGene

EG10980. sucB.

Phylogenomic databases

eggNOG

COG0508.

GeneTree

EBGT00050000011101.

HOGENOM

HBG630916.

OMA

AAMLTTY.

PhylomeDB

P0AFG6.

ProtClustDB

PRK05704.

Enzyme and pathway databases

BioCyc

EcoCyc:E2O-MONOMER.
MetaCyc:E2O-MONOMER.

Gene expression databases

Genevestigator

P0AFG6.

Family and domain databases

InterPro

IPR003016. 2-oxoA_DH_lipoyl-BS.
IPR001078. 2-oxoacid_DH_actylTfrase.
IPR000089. Biotin_lipoyl.
IPR023213. CAT-like_dom.
IPR004167. E3-bd.
IPR011053. Single_hybrid_motif.
IPR006255. SucB.
[Graphical view]

Gene3D

G3DSA:3.30.559.10. CAT-like_dom. 1 hit.
G3DSA:4.10.320.10. E3_bd. 1 hit.

KO

K00658.

Pfam

PF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]

SUPFAM

SSF47005. E3_bd. 1 hit.
SSF51230. Hybrid_motif. 1 hit.

TIGRFAMs

TIGR01347. SucB. 1 hit.

PROSITE

PS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

ODO2_ECOLI

Accession

Primary (citable) accession number: P0AFG6
Secondary accession number(s): P07016

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 68 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program