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Q8NRC3

- ODO12_CORGL

UniProt

Q8NRC3 - ODO12_CORGL

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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: 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

Pathwayi

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

  1. dihydrolipoyllysine-residue succinyltransferase activity Source: UniProtKB-EC
  2. metal ion binding Source: UniProtKB-KW
  3. oxoglutarate dehydrogenase (succinyl-transferring) activity Source: UniProtKB-EC
  4. thiamine pyrophosphate binding Source: InterPro

GO - Biological processi

  1. tricarboxylic acid cycle Source: UniProtKB-UniPathway
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 lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeCorynebacteriaceaeCorynebacterium
ProteomesiUP000000582: Chromosome, UP000001009: 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.
YP_225421.2. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB98522; BAB98522; BAB98522.
CAF19835; CAF19835; cg1280.
GeneIDi1019114.
3343144.
KEGGicgl: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.
RefSeqi NP_600357.3. NC_003450.3.
YP_225421.2. NC_006958.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q8NRC3. 1 interaction.
MINTi MINT-7713226.
STRINGi 196627.cg1280.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAB98522 ; BAB98522 ; BAB98522 .
CAF19835 ; CAF19835 ; cg1280 .
GeneIDi 1019114.
3343144.
KEGGi cgl:NCgl1084.
PATRICi 21494302. VBICorGlu203724_1108.

Phylogenomic databases

eggNOGi COG0508.
HOGENOMi HOG000259587.
KOi K00164.
OrthoDBi EOG6V1M1F.

Enzyme and pathway databases

UniPathwayi UPA00223 ; UER00997 .
BioCyci CGLU196627:GJDM-1116-MONOMER.

Family and domain databases

Gene3Di 3.30.559.10. 1 hit.
3.40.50.970. 2 hits.
InterProi IPR001078. 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 ]
PANTHERi PTHR23152. PTHR23152. 1 hit.
Pfami PF00198. 2-oxoacid_dh. 1 hit.
PF00676. E1_dh. 1 hit.
PF02779. Transket_pyr. 1 hit.
[Graphical view ]
PIRSFi PIRSF000157. Oxoglu_dh_E1. 1 hit.
SMARTi SM00861. Transket_pyr. 1 hit.
[Graphical view ]
SUPFAMi SSF52518. SSF52518. 2 hits.
TIGRFAMsi TIGR00239. 2oxo_dh_E1. 1 hit.
ProtoNeti Search...

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: November 26, 2014
This is version 91 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