Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

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P0AFG6 (ODO2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 82. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome] [HAMAP]

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	L-lysine catabolic process to acetyl-CoA via saccharopine Inferred from electronic annotation. Source: UniProtKB-UniPathway tricarboxylic acid cycle Inferred from mutant phenotype PubMed 6284701. Source: EcoliWiki
Cellular_component	oxoglutarate dehydrogenase complex Inferred from direct assay PubMed 5335914. Source: EcoliWiki
Molecular_function	dihydrolipoyllysine-residue succinyltransferase activity Inferred from direct assay PubMed 5335914. Source: EcoliWiki lipoic acid binding Inferred from direct assay PubMed 1854331. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.7

Chain

2 – 405

404

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

PRO_0000162262

Regions

Domain

2 – 77

Lipoyl-binding

Sites

Active site

376

Active site

380

Amino acid modifications

Modified residue

N6-lipoyllysine

Modified residue

148

N6-acetyllysine Ref.9

Secondary structure

405

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0AFG6 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 8439E48C6D381277
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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

« Hide

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] [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. 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]	"A role of RnlA in the RNase LS activity from Escherichia coli." Otsuka Y., Koga M., Iwamoto A., Yonesaki T. Genes Genet. Syst. 82:291-299(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 4-10. Strain: K12.
[5]	"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.
[6]	"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 1-12.
[7]	"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 2-13. Strain: K12 / EMG2.
[8]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[9]	"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] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-148, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[10]	"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] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 1-81.
[11]	"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] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 104-153.
[12]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405.
[13]	"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] [Europe PMC] [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.
YP_489006.1. NC_007779.1.

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.

STRING

511145.b0727.

2D gel databases

SWISS-2DPAGE

P0AFG6.

Proteomic databases

PaxDb

P0AFG6.

PRIDE

P0AFG6.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.

GeneID

12930951.
945307.

KEGG

ecj:Y75_p0706.
eco:b0727.

PATRIC

32116649. VBIEscCol129921_0757.

Organism-specific databases

EchoBASE

EB0973.

EcoGene

EG10980. sucB.

Phylogenomic databases

eggNOG

COG0508.

HOGENOM

HOG000281563.

K00658.

OMA

AAMLTTY.

ProtClustDB

PRK05704.

Enzyme and pathway databases

BioCyc

EcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.

UniPathway

UPA00868; UER00840.

Gene expression databases

Genevestigator

P0AFG6.

Family and domain databases

Gene3D

3.30.559.10. 1 hit.
4.10.320.10. 1 hit.

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]

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...

Other

EvolutionaryTrace

P0AFG6.

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:	May 1, 2013
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents