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P0AFG6 (ODO2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length405 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

sucAP0AFG35EBI-558621,EBI-543523

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.7
Chain2 – 405404Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
PRO_0000162262

Regions

Domain2 – 7776Lipoyl-binding

Sites

Active site3761
Active site3801

Amino acid modifications

Modified residue441N6-lipoyllysine
Modified residue1481N6-acetyllysine Ref.9

Secondary structure

............................................................. 405
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AFG6 [UniParc].

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

FASTA40544,011
        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' 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. expand/collapse author list , 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 277:1453-1462(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, IDENTIFICATION BY 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.
PIRXUECSD. F64808.
RefSeqNP_415255.1. NC_000913.3.
YP_489006.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BALNMR-A104-153[»]
1BBLNMR-A104-153[»]
1C4TX-ray3.00A/B/C173-405[»]
1E2OX-ray3.00A173-405[»]
1PMRNMR-A2-81[»]
1SCZX-ray2.20A173-405[»]
1W4HNMR-A109-153[»]
2BTGNMR-A109-153[»]
2BTHNMR-A109-153[»]
2WXCNMR-A109-153[»]
ProteinModelPortalP0AFG6.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-35787N.
IntActP0AFG6. 39 interactions.
MINTMINT-1242608.
STRING511145.b0727.

2D gel databases

SWISS-2DPAGEP0AFG6.

Proteomic databases

PaxDbP0AFG6.
PRIDEP0AFG6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.
GeneID12930951.
945307.
KEGGecj:Y75_p0706.
eco:b0727.
PATRIC32116649. VBIEscCol129921_0757.

Organism-specific databases

EchoBASEEB0973.
EcoGeneEG10980. sucB.

Phylogenomic databases

eggNOGCOG0508.
HOGENOMHOG000281563.
KOK00658.
OMAMMSTPIV.
OrthoDBEOG610413.
PhylomeDBP0AFG6.

Enzyme and pathway databases

BioCycEcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.
UniPathwayUPA00868; UER00840.

Gene expression databases

GenevestigatorP0AFG6.

Family and domain databases

Gene3D3.30.559.10. 1 hit.
4.10.320.10. 1 hit.
InterProIPR003016. 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]
PfamPF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]
SUPFAMSSF47005. SSF47005. 1 hit.
SSF51230. SSF51230. 1 hit.
TIGRFAMsTIGR01347. sucB. 1 hit.
PROSITEPS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0AFG6.
PROP0AFG6.

Entry information

Entry nameODO2_ECOLI
AccessionPrimary (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: July 9, 2014
This is version 90 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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