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P0AFG6

- ODO2_ECOLI

UniProt

P0AFG6 - ODO2_ECOLI

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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: 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

Binds 1 lipoyl cofactor covalently.

Pathwayi

Sites

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

GO - Molecular functioni

  1. dihydrolipoyllysine-residue succinyltransferase activity Source: EcoliWiki
  2. lipoic acid binding Source: EcoliWiki

GO - Biological processi

  1. L-lysine catabolic process to acetyl-CoA via saccharopine Source: UniProtKB-UniPathway
  2. 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.
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: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10980. sucB.

Subcellular locationi

GO - Cellular componenti

  1. 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-lipoyllysine1 Publication
Modified residuei148 – 1481N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP0AFG6.
PRIDEiP0AFG6.

2D gel databases

SWISS-2DPAGEP0AFG6.

Expressioni

Gene expression databases

GenevestigatoriP0AFG6.

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 – 344
Beta strandi42 – 443
Beta strandi70 – 767
Beta strandi105 – 1073
Helixi116 – 1183
Helixi121 – 1244
Helixi129 – 1313
Beta strandi136 – 1394
Helixi143 – 1464
Turni147 – 1493
Beta strandi176 – 1783
Helixi183 – 19614
Beta strandi201 – 2099
Helixi211 – 22818
Helixi235 – 24814
Turni250 – 2534
Beta strandi255 – 2573
Beta strandi260 – 2623
Beta strandi269 – 2713
Beta strandi273 – 2753
Beta strandi278 – 2803
Helixi287 – 2893
Helixi292 – 30514
Turni306 – 3094
Helixi313 – 3164
Beta strandi320 – 3256
Helixi326 – 3294
Beta strandi343 – 35816
Beta strandi361 – 37515
Turni376 – 3783
Helixi381 – 39616
Helixi400 – 4034

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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
Domaini2 – 7776Lipoyl-bindingAdd
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Lipoyl

Phylogenomic databases

eggNOGiCOG0508.
HOGENOMiHOG000281563.
InParanoidiP0AFG6.
KOiK00658.
OMAiMMSTPIV.
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:
EMBL
GenBank
DDBJ
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.
YP_489006.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.
GeneIDi12930951.
945307.
KEGGiecj:Y75_p0706.
eco:b0727.
PATRICi32116649. VBIEscCol129921_0757.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi F64808. XUECSD.
RefSeqi NP_415255.1. NC_000913.3.
YP_489006.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali P0AFG6.
SMRi P0AFG6. Positions 2-81, 104-153, 173-405.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-35787N.
IntActi P0AFG6. 39 interactions.
MINTi MINT-1242608.
STRINGi 511145.b0727.

2D gel databases

SWISS-2DPAGE P0AFG6.

Proteomic databases

PaxDbi P0AFG6.
PRIDEi P0AFG6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73821 ; AAC73821 ; b0727 .
BAA35393 ; BAA35393 ; BAA35393 .
GeneIDi 12930951.
945307.
KEGGi ecj:Y75_p0706.
eco:b0727.
PATRICi 32116649. VBIEscCol129921_0757.

Organism-specific databases

EchoBASEi EB0973.
EcoGenei EG10980. sucB.

Phylogenomic databases

eggNOGi COG0508.
HOGENOMi HOG000281563.
InParanoidi P0AFG6.
KOi K00658.
OMAi MMSTPIV.
OrthoDBi EOG610413.
PhylomeDBi P0AFG6.

Enzyme and pathway databases

UniPathwayi UPA00868 ; UER00840 .
BioCyci EcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0AFG6.
PROi P0AFG6.

Gene expression databases

Genevestigatori P0AFG6.

Family and domain databases

Gene3Di 3.30.559.10. 1 hit.
4.10.320.10. 1 hit.
InterProi 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 ]
Pfami PF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view ]
SUPFAMi SSF47005. SSF47005. 1 hit.
SSF51230. SSF51230. 1 hit.
TIGRFAMsi TIGR01347. sucB. 1 hit.
PROSITEi PS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: October 29, 2014
This is version 93 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