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Protein

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

Gene

sucB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.

Cofactori

(R)-lipoateNote: Binds 1 lipoyl cofactor covalently.

Pathway:iL-lysine degradation via saccharopine pathway

This protein is involved in step 6 of the subpathway that synthesizes glutaryl-CoA from L-lysine.
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  4. no protein annotated in this organism
  5. no protein annotated in this organism
  6. Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (sucB)
This subpathway is part of the pathway L-lysine degradation via saccharopine pathway, which is itself part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes glutaryl-CoA from L-lysine, the pathway L-lysine degradation via saccharopine pathway and in Amino-acid degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei376 – 3761
Active sitei380 – 3801

GO - Molecular functioni

  • dihydrolipoyllysine-residue succinyltransferase activity Source: EcoliWiki
  • lipoic acid binding Source: EcoliWiki

GO - Biological processi

  • L-lysine catabolic process to acetyl-CoA via saccharopine Source: UniProtKB-UniPathway
  • tricarboxylic acid cycle Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Tricarboxylic acid cycle

Enzyme and pathway databases

BioCyciEcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.
BRENDAi2.3.1.61. 2026.
UniPathwayiUPA00868; UER00840.

Names & Taxonomyi

Protein namesi
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 namesi
Name:sucB
Ordered Locus Names:b0727, JW0716
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10980. sucB.

Subcellular locationi

GO - Cellular componenti

  • oxoglutarate dehydrogenase complex Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 405404Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complexPRO_0000162262Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei44 – 441N6-lipoyllysinePROSITE-ProRule annotation1 Publication
Modified residuei148 – 1481N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP0AFG6.
PRIDEiP0AFG6.

2D gel databases

SWISS-2DPAGEP0AFG6.

Interactioni

Subunit structurei

Forms a 24-polypeptide structural core with octahedral symmetry.

Binary interactionsi

WithEntry#Exp.IntActNotes
sucAP0AFG35EBI-558621,EBI-543523

Protein-protein interaction databases

DIPiDIP-35787N.
IntActiP0AFG6. 39 interactions.
MINTiMINT-1242608.
STRINGi511145.b0727.

Structurei

Secondary structure

1
405
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi31 – 344Combined sources
Beta strandi42 – 443Combined sources
Beta strandi70 – 767Combined sources
Beta strandi105 – 1073Combined sources
Helixi116 – 1183Combined sources
Helixi121 – 1244Combined sources
Helixi129 – 1313Combined sources
Beta strandi136 – 1394Combined sources
Helixi143 – 1464Combined sources
Turni147 – 1493Combined sources
Beta strandi176 – 1783Combined sources
Helixi183 – 19614Combined sources
Beta strandi201 – 2099Combined sources
Helixi211 – 22818Combined sources
Helixi235 – 24814Combined sources
Turni250 – 2534Combined sources
Beta strandi255 – 2573Combined sources
Beta strandi260 – 2623Combined sources
Beta strandi269 – 2713Combined sources
Beta strandi273 – 2753Combined sources
Beta strandi278 – 2803Combined sources
Helixi287 – 2893Combined sources
Helixi292 – 30514Combined sources
Turni306 – 3094Combined sources
Helixi313 – 3164Combined sources
Beta strandi320 – 3256Combined sources
Helixi326 – 3294Combined sources
Beta strandi343 – 35816Combined sources
Beta strandi361 – 37515Combined sources
Turni376 – 3783Combined sources
Helixi381 – 39616Combined sources
Helixi400 – 4034Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0AFG6.
SMRiP0AFG6. Positions 2-81, 104-153, 173-405.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFG6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 7876Lipoyl-bindingPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the 2-oxoacid dehydrogenase family.Curated
Contains 1 lipoyl-binding domain.PROSITE-ProRule annotationCurated

Keywords - Domaini

Lipoyl

Phylogenomic databases

eggNOGiCOG0508.
HOGENOMiHOG000281563.
InParanoidiP0AFG6.
KOiK00658.
OMAiTFGKKAR.
OrthoDBiEOG610413.
PhylomeDBiP0AFG6.

Family and domain databases

Gene3Di3.30.559.10. 1 hit.
4.10.320.10. 1 hit.
InterProiIPR003016. 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]
PfamiPF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]
SUPFAMiSSF47005. SSF47005. 1 hit.
SSF51230. SSF51230. 1 hit.
TIGRFAMsiTIGR01347. sucB. 1 hit.
PROSITEiPS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AFG6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSVDILVPD LPESVADATV ATWHKKPGDA VVRDEVLVEI ETDKVVLEVP
60 70 80 90 100
ASADGILDAV LEDEGTTVTS RQILGRLREG NSAGKETSAK SEEKASTPAQ
110 120 130 140 150
RQQASLEEQN NDALSPAIRR LLAEHNLDAS AIKGTGVGGR LTREDVEKHL
160 170 180 190 200
AKAPAKESAP AAAAPAAQPA LAARSEKRVP MTRLRKRVAE RLLEAKNSTA
210 220 230 240 250
MLTTFNEVNM KPIMDLRKQY GEAFEKRHGI RLGFMSFYVK AVVEALKRYP
260 270 280 290 300
EVNASIDGDD VVYHNYFDVS MAVSTPRGLV TPVLRDVDTL GMADIEKKIK
310 320 330 340 350
ELAVKGRDGK LTVEDLTGGN FTITNGGVFG SLMSTPIINP PQSAILGMHA
360 370 380 390 400
IKDRPMAVNG QVEILPMMYL ALSYDHRLID GRESVGFLVT IKELLEDPTR

LLLDV
Length:405
Mass (Da):44,011
Last modified:January 23, 2007 - v2
Checksum:i8439E48C6D381277
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiF64808. XUECSD.
RefSeqiNP_415255.1. NC_000913.3.
WP_000099823.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.
GeneIDi945307.
KEGGieco:b0727.
PATRICi32116649. VBIEscCol129921_0757.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiF64808. XUECSD.
RefSeqiNP_415255.1. NC_000913.3.
WP_000099823.1. NZ_CP010445.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0AFG6.
SMRiP0AFG6. Positions 2-81, 104-153, 173-405.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-35787N.
IntActiP0AFG6. 39 interactions.
MINTiMINT-1242608.
STRINGi511145.b0727.

2D gel databases

SWISS-2DPAGEP0AFG6.

Proteomic databases

PaxDbiP0AFG6.
PRIDEiP0AFG6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.
GeneIDi945307.
KEGGieco:b0727.
PATRICi32116649. VBIEscCol129921_0757.

Organism-specific databases

EchoBASEiEB0973.
EcoGeneiEG10980. sucB.

Phylogenomic databases

eggNOGiCOG0508.
HOGENOMiHOG000281563.
InParanoidiP0AFG6.
KOiK00658.
OMAiTFGKKAR.
OrthoDBiEOG610413.
PhylomeDBiP0AFG6.

Enzyme and pathway databases

UniPathwayiUPA00868; UER00840.
BioCyciEcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.
BRENDAi2.3.1.61. 2026.

Miscellaneous databases

EvolutionaryTraceiP0AFG6.
PROiP0AFG6.

Family and domain databases

Gene3Di3.30.559.10. 1 hit.
4.10.320.10. 1 hit.
InterProiIPR003016. 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]
PfamiPF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]
SUPFAMiSSF47005. SSF47005. 1 hit.
SSF51230. SSF51230. 1 hit.
TIGRFAMsiTIGR01347. sucB. 1 hit.
PROSITEiPS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. 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, LIPOYLATION AT LYS-44.
  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.

Entry informationi

Entry nameiODO2_ECOLI
AccessioniPrimary (citable) accession number: P0AFG6
Secondary accession number(s): P07016
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: July 22, 2015
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.