ODO12_CORGL
ID ODO12_CORGL Reviewed; 1221 AA.
AC Q8NRC3; P96746; Q6M641;
DT 23-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 28-NOV-2012, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=2-oxoglutarate dehydrogenase E1/E2 component;
DE Short=ODH E1/E2 component;
DE Includes:
DE RecName: Full=2-oxoglutarate dehydrogenase E1 component;
DE Short=ODH E1 component;
DE EC=1.2.4.2 {ECO:0000269|PubMed:20675489, ECO:0000269|PubMed:9004499};
DE AltName: Full=Alpha-ketoglutarate dehydrogenase E1 component;
DE Short=KDH E1 component;
DE Includes:
DE RecName: Full=Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex;
DE EC=2.3.1.61 {ECO:0000269|PubMed:20675489};
DE AltName: Full=2-oxoglutarate dehydrogenase complex E2 component;
DE Short=ODH E2 component;
DE Short=OGDC-E2;
DE AltName: Full=Dihydrolipoamide succinyltransferase;
GN Name=odhA {ECO:0000312|EMBL:CAF19835.1}; OrderedLocusNames=Cgl1129, cg1280;
OS Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 /
OS JCM 1318 / LMG 3730 / NCIMB 10025).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=196627;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CATALYTIC ACTIVITY.
RC STRAIN=AJ12036;
RX PubMed=9004499; DOI=10.1099/13500872-142-12-3347;
RA Usuda Y., Tujimoto N., Abe C., Asakura Y., Kimura E., Kawahara Y.,
RA Kurahashi O., Matsui H.;
RT "Molecular cloning of the Corynebacterium glutamicum ('Brevibacterium
RT lactofermentum' AJ12036) odhA gene encoding a novel type of 2-oxoglutarate
RT dehydrogenase.";
RL Microbiology 142:3347-3354(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12743753; DOI=10.1007/s00253-003-1328-1;
RA Ikeda M., Nakagawa S.;
RT "The Corynebacterium glutamicum genome: features and impacts on
RT biotechnological processes.";
RL Appl. Microbiol. Biotechnol. 62:99-109(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025 {ECO:0000312|EMBL:CAF19835.1};
RX PubMed=12948626; DOI=10.1016/s0168-1656(03)00154-8;
RA Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A.,
RA Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A.,
RA Hartmann M., Huthmacher K., Kraemer R., Linke B., McHardy A.C., Meyer F.,
RA Moeckel B., Pfefferle W., Puehler A., Rey D.A., Rueckert C., Rupp O.,
RA Sahm H., Wendisch V.F., Wiegraebe I., Tauch A.;
RT "The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its
RT impact on the production of L-aspartate-derived amino acids and vitamins.";
RL J. Biotechnol. 104:5-25(2003).
RN [4]
RP PROTEIN SEQUENCE OF 2-8, FUNCTION AS E1 AND E2 COMPONENT OF ODH, CATALYTIC
RP ACTIVITY, KINETIC PARAMETERS, DOMAIN, LACK OF LIPOYLATION, ACTIVE SITE, AND
RP MUTAGENESIS OF THR-258; HIS-316 AND GLN-320.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=20675489; DOI=10.1128/jb.00597-10;
RA Hoffelder M., Raasch K., van Ooyen J., Eggeling L.;
RT "The E2 domain of OdhA of Corynebacterium glutamicum has
RT succinyltransferase activity dependent on lipoyl residues of the
RT acetyltransferase AceF.";
RL J. Bacteriol. 192:5203-5211(2010).
RN [5]
RP INHIBITION BY ODHI, AND IDENTIFICATION IN THE ODH/PDH COMPLEX.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=16522631; DOI=10.1074/jbc.m512515200;
RA Niebisch A., Kabus A., Schultz C., Weil B., Bott M.;
RT "Corynebacterial protein kinase G controls 2-oxoglutarate dehydrogenase
RT activity via the phosphorylation status of the OdhI protein.";
RL J. Biol. Chem. 281:12300-12307(2006).
RN [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 13869 / DSMZ 1412 / NCIMB 9567;
RX PubMed=17158630; DOI=10.1128/aem.01867-06;
RA Asakura Y., Kimura E., Usuda Y., Kawahara Y., Matsui K., Osumi T.,
RA Nakamatsu T.;
RT "Altered metabolic flux due to deletion of odhA causes L-glutamate
RT overproduction in Corynebacterium glutamicum.";
RL Appl. Environ. Microbiol. 73:1308-1319(2007).
RN [7]
RP DOMAIN, ACTIVITY REGULATION, AND INTERACTION WITH ODHI.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=20303957; DOI=10.1016/j.febslet.2010.03.028;
RA Krawczyk S., Raasch K., Schultz C., Hoffelder M., Eggeling L., Bott M.;
RT "The FHA domain of OdhI interacts with the carboxyterminal 2-oxoglutarate
RT dehydrogenase domain of OdhA in Corynebacterium glutamicum.";
RL FEBS Lett. 584:1463-1468(2010).
CC -!- FUNCTION: Catalyzes the E1 and E2 reactions as part of 2-oxoglutarate
CC dehydrogenase (ODH) activity, to convert 2-oxoglutarate to succinyl-CoA
CC and CO(2). OdhA has reductase activity with 2-oxoglutarate but does not
CC react with pyruvate, and also displays transsuccinylase but no
CC transacetylase activity. Since OdhA is not lipoylated, the
CC succinyltransferase activity of its E2 domain is dependent on lipoyl
CC residues of the acetyltransferase AceF. {ECO:0000269|PubMed:20675489}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-lipoyl-L-lysyl-[dihydrolipoyllysine-residue
CC succinyltransferase] + 2-oxoglutarate + H(+) = (R)-N(6)-(S(8)-
CC succinyldihydrolipoyl)-L-lysyl-[dihydrolipoyllysine-residue
CC succinyltransferase] + CO2; Xref=Rhea:RHEA:12188, Rhea:RHEA-
CC COMP:10483, Rhea:RHEA-COMP:10484, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:83099,
CC ChEBI:CHEBI:83120; EC=1.2.4.2; Evidence={ECO:0000269|PubMed:20675489,
CC ECO:0000269|PubMed:9004499};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-dihydrolipoyl-L-lysyl-[2-oxoglutarate dehydrogenase
CC complex component E2] + succinyl-CoA = (R)-N(6)-(S(8)-
CC succinyldihydrolipoyl)-L-lysyl-[2-oxoglutarate dehydrogenase complex
CC component E2] + CoA; Xref=Rhea:RHEA:15213, Rhea:RHEA-COMP:10581,
CC Rhea:RHEA-COMP:10582, ChEBI:CHEBI:57287, ChEBI:CHEBI:57292,
CC ChEBI:CHEBI:83100, ChEBI:CHEBI:83120; EC=2.3.1.61;
CC Evidence={ECO:0000269|PubMed:20675489};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000250|UniProtKB:P0AFG3};
CC -!- ACTIVITY REGULATION: Inhibited by unphosphorylated OdhI, but not by
CC phosphorylated OdhI. {ECO:0000269|PubMed:20303957}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.014 mM for 2-oxoglutarate {ECO:0000269|PubMed:20675489};
CC -!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; succinyl-
CC CoA from 2-oxoglutarate (dehydrogenase route): step 1/1.
CC -!- SUBUNIT: Homodimer (By similarity). Part of an unusual ODH/PDH
CC supercomplex, consisting of AceE (E1), AceF (E2), and Lpd (E3) together
CC with OdhA (E1+E2). Interacts with the FHA domain of unphosphorylated
CC OdhI via its C-terminal dehydrogenase domain. {ECO:0000250,
CC ECO:0000269|PubMed:16522631, ECO:0000269|PubMed:20303957}.
CC -!- INTERACTION:
CC Q8NRC3; Q8NQJ3: odhI; NbExp=2; IntAct=EBI-7868591, EBI-7868645;
CC -!- DOMAIN: OdhA is a fusion protein with two major domains exhibiting
CC structural features of an E1 and E2 protein, and a short sequence
CC stretch of E1 localized at the N-terminus, which is connected by a
CC linker region to the rest of the protein. Deletion of individual parts
CC of odhA show that all parts of odhA are required for a functional
CC tricarboxylic acid cycle in C.glutamicum; the ODH activity is in fact
CC completely abolished in each of these mutants, and the PDH activity is
CC significantly reduced, which could indicate that the overall structure
CC of the supercomplex is disturbed. {ECO:0000269|PubMed:20303957,
CC ECO:0000269|PubMed:20675489}.
CC -!- DISRUPTION PHENOTYPE: Strains lacking this gene completely lack 2-
CC oxoglutarate dehydrogenase activity. Deletion of odhA also causes L-
CC glutamate overproduction and accumulation during growth.
CC {ECO:0000269|PubMed:17158630}.
CC -!- MISCELLANEOUS: Is non-lipoylated. In contrast, the E2 component AceF is
CC the prominent lipoylated protein in C.glutamicum.
CC -!- SIMILARITY: In the N-terminal section; belongs to the alpha-
CC ketoglutarate dehydrogenase family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the 2-oxoacid
CC dehydrogenase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB98522.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAF19835.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; D84102; BAA12222.2; -; Genomic_DNA.
DR EMBL; BA000036; BAB98522.1; ALT_INIT; Genomic_DNA.
DR EMBL; BX927151; CAF19835.1; ALT_INIT; Genomic_DNA.
DR RefSeq; NP_600357.3; NC_003450.3.
DR RefSeq; WP_011014138.1; NC_006958.1.
DR AlphaFoldDB; Q8NRC3; -.
DR SMR; Q8NRC3; -.
DR IntAct; Q8NRC3; 1.
DR MINT; Q8NRC3; -.
DR STRING; 196627.cg1280; -.
DR PRIDE; Q8NRC3; -.
DR KEGG; cgb:cg1280; -.
DR KEGG; cgl:Cgl1129; -.
DR PATRIC; fig|196627.13.peg.1108; -.
DR eggNOG; COG0508; Bacteria.
DR eggNOG; COG0567; Bacteria.
DR HOGENOM; CLU_004709_1_0_11; -.
DR BRENDA; 1.2.1.105; 960.
DR SABIO-RK; Q8NRC3; -.
DR UniPathway; UPA00223; UER00997.
DR Proteomes; UP000000582; Chromosome.
DR GO; GO:0004149; F:dihydrolipoyllysine-residue succinyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProt.
DR GO; GO:0004591; F:oxoglutarate dehydrogenase (succinyl-transferring) activity; IEA:UniProtKB-EC.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:InterPro.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.559.10; -; 1.
DR Gene3D; 3.40.50.11610; -; 1.
DR InterPro; IPR001078; 2-oxoacid_DH_actylTfrase.
DR InterPro; IPR032106; 2-oxogl_dehyd_N.
DR InterPro; IPR011603; 2oxoglutarate_DH_E1.
DR InterPro; IPR023213; CAT-like_dom_sf.
DR InterPro; IPR001017; DH_E1.
DR InterPro; IPR031717; KGD_C.
DR InterPro; IPR042179; KGD_C_sf.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR005475; Transketolase-like_Pyr-bd.
DR PANTHER; PTHR23152; PTHR23152; 1.
DR Pfam; PF00198; 2-oxoacid_dh; 1.
DR Pfam; PF16078; 2-oxogl_dehyd_N; 1.
DR Pfam; PF00676; E1_dh; 1.
DR Pfam; PF16870; OxoGdeHyase_C; 1.
DR Pfam; PF02779; Transket_pyr; 1.
DR PIRSF; PIRSF000157; Oxoglu_dh_E1; 1.
DR SMART; SM00861; Transket_pyr; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR TIGRFAMs; TIGR00239; 2oxo_dh_E1; 1.
PE 1: Evidence at protein level;
KW Acyltransferase; Direct protein sequencing; Magnesium; Metal-binding;
KW Multifunctional enzyme; Oxidoreductase; Reference proteome;
KW Thiamine pyrophosphate; Transferase; Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:20675489"
FT CHAIN 2..1221
FT /note="2-oxoglutarate dehydrogenase E1/E2 component"
FT /id="PRO_0000273521"
FT REGION 2..40
FT /note="2-oxoglutarate dehydrogenase E1, N-terminal part"
FT REGION 22..107
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 41..89
FT /note="Linker"
FT REGION 90..337
FT /note="Succinyltransferase E2"
FT REGION 338..1221
FT /note="2-oxoglutarate dehydrogenase E1, C-terminal part"
FT COMPBIAS 22..36
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 41..55
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 316
FT /note="Proton acceptor; for succinyltransferase activity"
FT /evidence="ECO:0000269|PubMed:20675489"
FT BINDING 543..544
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 583
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250"
FT BINDING 608..610
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 608
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250"
FT BINDING 645..647
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 645
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 678
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 680
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 949
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 1017
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250"
FT MUTAGEN 258
FT /note="T->A: Loss of E2 succinyltransferase activity, but
FT nearly no effect on E1 dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:20675489"
FT MUTAGEN 316
FT /note="H->C: Loss of E2 succinyltransferase activity, and
FT 2-fold reduction in E1 dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:20675489"
FT MUTAGEN 320
FT /note="Q->D: Slight reduction in E2 succinyltransferase
FT activity and in E1 dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:20675489"
FT CONFLICT 44
FT /note="T -> A (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
FT CONFLICT 82
FT /note="D -> A (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
FT CONFLICT 238
FT /note="A -> T (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
FT CONFLICT 413
FT /note="N -> S (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
FT CONFLICT 424
FT /note="N -> S (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
FT CONFLICT 967
FT /note="I -> V (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
FT CONFLICT 1093
FT /note="N -> D (in Ref. 1; BAA12222)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1221 AA; 134664 MW; BF0A1827EA1B0080 CRC64;
MSSASTFGQN AWLVDEMFQQ FQKDPKSVDK EWRELFEAQG GPNTTPATTE AQPSAPKESA
KPAPKAAPAA KAAPRVETKP ADKTAPKAKE SSVPQQPKLP EPGQTPIRGI FKSIAKNMDI
SLEIPTATSV RDMPARLMFE NRAMVNDQLK RTRGGKISFT HIIGYAMVKA VMAHPDMNNS
YDVIDGKPTL IVPEHINLGL AIDLPQKDGS RALVVAAIKE TEKMNFSEFL AAYEDIVARS
RKGKLTMDDY QGVTVSLTNP GGIGTRHSVP RLTKGQGTII GVGSMDYPAE FQGASEDRLA
ELGVGKLVTI TSTYDHRVIQ GAVSGEFLRT MSRLLTDDSF WDEIFDAMNV PYTPMRWAQD
VPNTGVDKNT RVMQLIEAYR SRGHLIADTN PLSWVQPGMP VPDHRDLDIE THNLTIWDLD
RTFNVGGFGG KETMTLREVL SRLRAAYTLK VGSEYTHILD RDERTWLQDR LEAGMPKPTQ
AEQKYILQKL NAAEAFENFL QTKYVGQKRF SLEGAEALIP LMDSAIDTAA GQGLDEVVIG
MPHRGRLNVL FNIVGKPLAS IFNEFEGQME QGQIGGSGDV KYHLGSEGQH LQMFGDGEIK
VSLTANPSHL EAVNPVMEGI VRAKQDYLDK GVDGKTVVPL LLHGDAAFAG LGIVPETINL
AKLRGYDVGG TIHIVVNNQI GFTTTPDSSR SMHYATDYAK AFGCPVFHVN GDDPEAVVWV
GQLATEYRRR FGKDVFIDLV CYRLRGHNEA DDPSMTQPKM YELITGRETV RAQYTEDLLG
RGDLSNEDAE AVVRDFHDQM ESVFNEVKEG GKKQAEAQTG ITGSQKLPHG LETNISREEL
LELGQAFANT PEGFNYHPRV APVAKKRVSS VTEGGIDWAW GELLAFGSLA NSGRLVRLAG
EDSRRGTFTQ RHAVAIDPAT AEEFNPLHEL AQSKGNNGKF LVYNSALTEY AGMGFEYGYS
VGNEDSIVAW EAQFGDFANG AQTIIDEYVS SGEAKWGQTS KLILLLPHGY EGQGPDHSSA
RIERFLQLCA EGSMTVAQPS TPANHFHLLR RHALSDLKRP LVIFTPKSML RNKAAASAPE
DFTEVTKFQS VINDPNVADA AKVKKVMLVS GKLYYELAKR KEKDGRDDIA IVRIEMLHPI
PFNRISEALA GYPNAEEVLF VQDEPANQGP WPFYQEHLPE LIPNMPKMRR VSRRAQSSTA
TGVAKVHQLE EKQLIDEAFE A
