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P0AFG6

- ODO2_ECOLI

UniProt

P0AFG6 - ODO2_ECOLI

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
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    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
    3. protein binding Source: IntAct

    GO - Biological processi

    1. L-lysine catabolic process to acetyl-CoA via saccharopine Source: UniProtKB-UniPathway
    2. tricarboxylic acid cycle Source: EcoliWiki

    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

    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.
    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.
    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

    MSSVDILVPD LPESVADATV ATWHKKPGDA VVRDEVLVEI ETDKVVLEVP    50
    ASADGILDAV LEDEGTTVTS RQILGRLREG NSAGKETSAK SEEKASTPAQ 100
    RQQASLEEQN NDALSPAIRR LLAEHNLDAS AIKGTGVGGR LTREDVEKHL 150
    AKAPAKESAP AAAAPAAQPA LAARSEKRVP MTRLRKRVAE RLLEAKNSTA 200
    MLTTFNEVNM KPIMDLRKQY GEAFEKRHGI RLGFMSFYVK AVVEALKRYP 250
    EVNASIDGDD VVYHNYFDVS MAVSTPRGLV TPVLRDVDTL GMADIEKKIK 300
    ELAVKGRDGK LTVEDLTGGN FTITNGGVFG SLMSTPIINP PQSAILGMHA 350
    IKDRPMAVNG QVEILPMMYL ALSYDHRLID GRESVGFLVT IKELLEDPTR 400
    LLLDV 405
    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.
    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.
    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

    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 1, 2014
    This is version 92 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