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Protein

2-oxoglutarate dehydrogenase E1/E2 component

Gene

odhA

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the E1 and E2 reactions as part of 2-oxoglutarate dehydrogenase (ODH) activity, to convert 2-oxoglutarate to succinyl-CoA and CO2. OdhA has reductase activity with 2-oxoglutarate but does not react with pyruvate, and also displays transsuccinylase but no transacetylase activity. Since OdhA is not lipoylated, the succinyltransferase activity of its E2 domain is dependent on lipoyl residues of the acetyltransferase AceF.1 Publication

Catalytic activityi

2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2.1 Publication
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarity
  • thiamine diphosphateBy similarity

Enzyme regulationi

Inhibited by unphosphorylated OdhI, but not by phosphorylated OdhI.1 Publication

Kineticsi

  1. KM=0.014 mM for 2-oxoglutarate1 Publication

    Pathway:itricarboxylic acid cycle

    This protein is involved in step 1 of the subpathway that synthesizes succinyl-CoA from 2-oxoglutarate (dehydrogenase route).
    Proteins known to be involved in this subpathway in this organism are:
    1. 2-oxoglutarate dehydrogenase E1/E2 component (odhA), Dihydrolipoyl dehydrogenase (lpd)
    This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes succinyl-CoA from 2-oxoglutarate (dehydrogenase route), the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei316 – 3161Proton acceptor; for succinyltransferase activity1 Publication
    Binding sitei583 – 58312-oxoglutarateBy similarity
    Binding sitei608 – 60812-oxoglutarateBy similarity
    Metal bindingi645 – 6451MagnesiumBy similarity
    Metal bindingi678 – 6781MagnesiumBy similarity
    Metal bindingi680 – 6801Magnesium; via carbonyl oxygenBy similarity
    Binding sitei949 – 9491Thiamine pyrophosphateBy similarity
    Binding sitei1017 – 101712-oxoglutarateBy similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Acyltransferase, Oxidoreductase, Transferase

    Keywords - Biological processi

    Tricarboxylic acid cycle

    Keywords - Ligandi

    Magnesium, Metal-binding, Thiamine pyrophosphate

    Enzyme and pathway databases

    BioCyciCGLU196627:GJDM-1116-MONOMER.
    UniPathwayiUPA00223; UER00997.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-oxoglutarate dehydrogenase E1/E2 component
    Short name:
    ODH E1/E2 component
    Including the following 2 domains:
    2-oxoglutarate dehydrogenase E1 component (EC:1.2.4.2)
    Short name:
    ODH E1 component
    Alternative name(s):
    Alpha-ketoglutarate dehydrogenase E1 component
    Short name:
    KDH E1 component
    Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (EC:2.3.1.61)
    Alternative name(s):
    2-oxoglutarate dehydrogenase complex E2 component
    Short name:
    ODH E2 component
    Short name:
    OGDC-E2
    Dihydrolipoamide succinyltransferase
    Gene namesi
    Name:odhAImported
    Ordered Locus Names:Cgl1129, cg1280
    OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
    Taxonomic identifieri196627 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
    ProteomesiUP000000582 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Strains lacking this gene completely lack 2-oxoglutarate dehydrogenase activity. Deletion of odhA also causes L-glutamate overproduction and accumulation during growth.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi258 – 2581T → A: Loss of E2 succinyltransferase activity, but nearly no effect on E1 dehydrogenase activity. 1 Publication
    Mutagenesisi316 – 3161H → C: Loss of E2 succinyltransferase activity, and 2-fold reduction in E1 dehydrogenase activity. 1 Publication
    Mutagenesisi320 – 3201Q → D: Slight reduction in E2 succinyltransferase activity and in E1 dehydrogenase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 122112202-oxoglutarate dehydrogenase E1/E2 componentPRO_0000273521Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer (By similarity). Part of an unusual ODH/PDH supercomplex, consisting of AceE (E1), AceF (E2), and Lpd (E3) together with OdhA (E1+E2). Interacts with the FHA domain of unphosphorylated OdhI via its C-terminal dehydrogenase domain.By similarity2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    odhIQ8NQJ32EBI-7868591,EBI-7868645

    Protein-protein interaction databases

    IntActiQ8NRC3. 1 interaction.
    MINTiMINT-7713226.
    STRINGi196627.cg1280.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni2 – 40392-oxoglutarate dehydrogenase E1, N-terminal partAdd
    BLAST
    Regioni41 – 8949LinkerAdd
    BLAST
    Regioni90 – 337248Succinyltransferase E2Add
    BLAST
    Regioni338 – 12218842-oxoglutarate dehydrogenase E1, C-terminal partAdd
    BLAST
    Regioni543 – 5442Thiamine pyrophosphate bindingBy similarity
    Regioni608 – 6103Thiamine pyrophosphate bindingBy similarity
    Regioni645 – 6473Thiamine pyrophosphate bindingBy similarity

    Domaini

    OdhA is a fusion protein with two major domains exhibiting structural features of an E1 and E2 protein, and a short sequence stretch of E1 localized at the N-terminus, which is connected by a linker region to the rest of the protein. Deletion of individual parts of odhA show that all parts of odhA are required for a functional tricarboxylic acid cycle in C.glutamicum; the ODH activity is in fact completely abolished in each of these mutants, and the PDH activity is significantly reduced, which could indicate that the overall structure of the supercomplex is disturbed.2 Publications

    Sequence similaritiesi

    In the N-terminal section; belongs to the alpha-ketoglutarate dehydrogenase family.Curated
    In the C-terminal section; belongs to the 2-oxoacid dehydrogenase family.Curated

    Phylogenomic databases

    eggNOGiCOG0508.
    HOGENOMiHOG000259587.
    KOiK00164.
    OrthoDBiEOG6V1M1F.

    Family and domain databases

    Gene3Di3.30.559.10. 1 hit.
    3.40.50.970. 2 hits.
    InterProiIPR001078. 2-oxoacid_DH_actylTfrase.
    IPR011603. 2oxoglutarate_DH_E1.
    IPR023213. CAT-like_dom.
    IPR001017. DH_E1.
    IPR029061. THDP-binding.
    IPR005475. Transketolase-like_Pyr-bd.
    [Graphical view]
    PANTHERiPTHR23152. PTHR23152. 1 hit.
    PfamiPF00198. 2-oxoacid_dh. 1 hit.
    PF00676. E1_dh. 1 hit.
    PF02779. Transket_pyr. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000157. Oxoglu_dh_E1. 1 hit.
    SMARTiSM00861. Transket_pyr. 1 hit.
    [Graphical view]
    SUPFAMiSSF52518. SSF52518. 2 hits.
    TIGRFAMsiTIGR00239. 2oxo_dh_E1. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q8NRC3-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSSASTFGQN AWLVDEMFQQ FQKDPKSVDK EWRELFEAQG GPNTTPATTE
    60 70 80 90 100
    AQPSAPKESA KPAPKAAPAA KAAPRVETKP ADKTAPKAKE SSVPQQPKLP
    110 120 130 140 150
    EPGQTPIRGI FKSIAKNMDI SLEIPTATSV RDMPARLMFE NRAMVNDQLK
    160 170 180 190 200
    RTRGGKISFT HIIGYAMVKA VMAHPDMNNS YDVIDGKPTL IVPEHINLGL
    210 220 230 240 250
    AIDLPQKDGS RALVVAAIKE TEKMNFSEFL AAYEDIVARS RKGKLTMDDY
    260 270 280 290 300
    QGVTVSLTNP GGIGTRHSVP RLTKGQGTII GVGSMDYPAE FQGASEDRLA
    310 320 330 340 350
    ELGVGKLVTI TSTYDHRVIQ GAVSGEFLRT MSRLLTDDSF WDEIFDAMNV
    360 370 380 390 400
    PYTPMRWAQD VPNTGVDKNT RVMQLIEAYR SRGHLIADTN PLSWVQPGMP
    410 420 430 440 450
    VPDHRDLDIE THNLTIWDLD RTFNVGGFGG KETMTLREVL SRLRAAYTLK
    460 470 480 490 500
    VGSEYTHILD RDERTWLQDR LEAGMPKPTQ AEQKYILQKL NAAEAFENFL
    510 520 530 540 550
    QTKYVGQKRF SLEGAEALIP LMDSAIDTAA GQGLDEVVIG MPHRGRLNVL
    560 570 580 590 600
    FNIVGKPLAS IFNEFEGQME QGQIGGSGDV KYHLGSEGQH LQMFGDGEIK
    610 620 630 640 650
    VSLTANPSHL EAVNPVMEGI VRAKQDYLDK GVDGKTVVPL LLHGDAAFAG
    660 670 680 690 700
    LGIVPETINL AKLRGYDVGG TIHIVVNNQI GFTTTPDSSR SMHYATDYAK
    710 720 730 740 750
    AFGCPVFHVN GDDPEAVVWV GQLATEYRRR FGKDVFIDLV CYRLRGHNEA
    760 770 780 790 800
    DDPSMTQPKM YELITGRETV RAQYTEDLLG RGDLSNEDAE AVVRDFHDQM
    810 820 830 840 850
    ESVFNEVKEG GKKQAEAQTG ITGSQKLPHG LETNISREEL LELGQAFANT
    860 870 880 890 900
    PEGFNYHPRV APVAKKRVSS VTEGGIDWAW GELLAFGSLA NSGRLVRLAG
    910 920 930 940 950
    EDSRRGTFTQ RHAVAIDPAT AEEFNPLHEL AQSKGNNGKF LVYNSALTEY
    960 970 980 990 1000
    AGMGFEYGYS VGNEDSIVAW EAQFGDFANG AQTIIDEYVS SGEAKWGQTS
    1010 1020 1030 1040 1050
    KLILLLPHGY EGQGPDHSSA RIERFLQLCA EGSMTVAQPS TPANHFHLLR
    1060 1070 1080 1090 1100
    RHALSDLKRP LVIFTPKSML RNKAAASAPE DFTEVTKFQS VINDPNVADA
    1110 1120 1130 1140 1150
    AKVKKVMLVS GKLYYELAKR KEKDGRDDIA IVRIEMLHPI PFNRISEALA
    1160 1170 1180 1190 1200
    GYPNAEEVLF VQDEPANQGP WPFYQEHLPE LIPNMPKMRR VSRRAQSSTA
    1210 1220
    TGVAKVHQLE EKQLIDEAFE A
    Length:1,221
    Mass (Da):134,664
    Last modified:November 28, 2012 - v2
    Checksum:iBF0A1827EA1B0080
    GO

    Sequence cautioni

    The sequence BAB98522.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence CAF19835.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti44 – 441T → A in BAA12222 (PubMed:9004499).Curated
    Sequence conflicti82 – 821D → A in BAA12222 (PubMed:9004499).Curated
    Sequence conflicti238 – 2381A → T in BAA12222 (PubMed:9004499).Curated
    Sequence conflicti413 – 4131N → S in BAA12222 (PubMed:9004499).Curated
    Sequence conflicti424 – 4241N → S in BAA12222 (PubMed:9004499).Curated
    Sequence conflicti967 – 9671I → V in BAA12222 (PubMed:9004499).Curated
    Sequence conflicti1093 – 10931N → D in BAA12222 (PubMed:9004499).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D84102 Genomic DNA. Translation: BAA12222.2.
    BA000036 Genomic DNA. Translation: BAB98522.1. Different initiation.
    BX927151 Genomic DNA. Translation: CAF19835.1. Different initiation.
    RefSeqiNP_600357.3. NC_003450.3.
    WP_011014138.1. NC_006958.1.

    Genome annotation databases

    EnsemblBacteriaiBAB98522; BAB98522; BAB98522.
    CAF19835; CAF19835; cg1280.
    GeneIDi1019114.
    KEGGicgb:cg1280.
    cgl:NCgl1084.
    PATRICi21494302. VBICorGlu203724_1108.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D84102 Genomic DNA. Translation: BAA12222.2.
    BA000036 Genomic DNA. Translation: BAB98522.1. Different initiation.
    BX927151 Genomic DNA. Translation: CAF19835.1. Different initiation.
    RefSeqiNP_600357.3. NC_003450.3.
    WP_011014138.1. NC_006958.1.

    3D structure databases

    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiQ8NRC3. 1 interaction.
    MINTiMINT-7713226.
    STRINGi196627.cg1280.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAB98522; BAB98522; BAB98522.
    CAF19835; CAF19835; cg1280.
    GeneIDi1019114.
    KEGGicgb:cg1280.
    cgl:NCgl1084.
    PATRICi21494302. VBICorGlu203724_1108.

    Phylogenomic databases

    eggNOGiCOG0508.
    HOGENOMiHOG000259587.
    KOiK00164.
    OrthoDBiEOG6V1M1F.

    Enzyme and pathway databases

    UniPathwayiUPA00223; UER00997.
    BioCyciCGLU196627:GJDM-1116-MONOMER.

    Family and domain databases

    Gene3Di3.30.559.10. 1 hit.
    3.40.50.970. 2 hits.
    InterProiIPR001078. 2-oxoacid_DH_actylTfrase.
    IPR011603. 2oxoglutarate_DH_E1.
    IPR023213. CAT-like_dom.
    IPR001017. DH_E1.
    IPR029061. THDP-binding.
    IPR005475. Transketolase-like_Pyr-bd.
    [Graphical view]
    PANTHERiPTHR23152. PTHR23152. 1 hit.
    PfamiPF00198. 2-oxoacid_dh. 1 hit.
    PF00676. E1_dh. 1 hit.
    PF02779. Transket_pyr. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000157. Oxoglu_dh_E1. 1 hit.
    SMARTiSM00861. Transket_pyr. 1 hit.
    [Graphical view]
    SUPFAMiSSF52518. SSF52518. 2 hits.
    TIGRFAMsiTIGR00239. 2oxo_dh_E1. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Molecular cloning of the Corynebacterium glutamicum ('Brevibacterium lactofermentum' AJ12036) odhA gene encoding a novel type of 2-oxoglutarate dehydrogenase."
      Usuda Y., Tujimoto N., Abe C., Asakura Y., Kimura E., Kawahara Y., Kurahashi O., Matsui H.
      Microbiology 142:3347-3354(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY.
      Strain: AJ12036.
    2. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
      Ikeda M., Nakagawa S.
      Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025Imported.
    4. "The E2 domain of OdhA of Corynebacterium glutamicum has succinyltransferase activity dependent on lipoyl residues of the acetyltransferase AceF."
      Hoffelder M., Raasch K., van Ooyen J., Eggeling L.
      J. Bacteriol. 192:5203-5211(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-8, FUNCTION AS E1 AND E2 COMPONENT OF ODH, CATALYTIC ACTIVITY, KINETIC PARAMETERS, DOMAIN, LACK OF LIPOYLATION, ACTIVE SITE, MUTAGENESIS OF THR-258; HIS-316 AND GLN-320.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    5. "Corynebacterial protein kinase G controls 2-oxoglutarate dehydrogenase activity via the phosphorylation status of the OdhI protein."
      Niebisch A., Kabus A., Schultz C., Weil B., Bott M.
      J. Biol. Chem. 281:12300-12307(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INHIBITION BY ODHI, IDENTIFICATION IN THE ODH/PDH COMPLEX.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    6. "Altered metabolic flux due to deletion of odhA causes L-glutamate overproduction in Corynebacterium glutamicum."
      Asakura Y., Kimura E., Usuda Y., Kawahara Y., Matsui K., Osumi T., Nakamatsu T.
      Appl. Environ. Microbiol. 73:1308-1319(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
      Strain: ATCC 13869 / DSMZ 1412 / NCIMB 9567.
    7. "The FHA domain of OdhI interacts with the carboxyterminal 2-oxoglutarate dehydrogenase domain of OdhA in Corynebacterium glutamicum."
      Krawczyk S., Raasch K., Schultz C., Hoffelder M., Eggeling L., Bott M.
      FEBS Lett. 584:1463-1468(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: DOMAIN, ENZYME REGULATION, INTERACTION WITH ODHI.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.

    Entry informationi

    Entry nameiODO12_CORGL
    AccessioniPrimary (citable) accession number: Q8NRC3
    Secondary accession number(s): P96746, Q6M641
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 23, 2007
    Last sequence update: November 28, 2012
    Last modified: July 22, 2015
    This is version 97 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Is non-lipoylated. In contrast, the E2 component AceF is the prominent lipoylated protein in C.glutamicum.

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. 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.