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A1TDK2

- KGD_MYCVP

UniProt

A1TDK2 - KGD_MYCVP

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Protein

Multifunctional 2-oxoglutarate metabolism enzyme

Gene
kgd, Mvan_4477
Organism
Mycobacterium vanbaalenii (strain DSM 7251 / PYR-1)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO2. The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle By similarity.

Catalytic activityi

2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO2.
2-oxoglutarate = succinate semialdehyde + CO2.
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2.
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.

Cofactori

Magnesium By similarity.
Thiamine pyrophosphate By similarity.

Enzyme regulationi

Alpha-ketoglutarate dehydrogenase and decarboxylase activities are inhibited by unphosphorylated GarA, and allosterically activated by acetyl-CoA, the main substrate of the TCA cycle By similarity.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei332 – 3321Proton acceptor; for succinyltransferase activity By similarity
Binding sitei597 – 59712-oxoglutarate By similarity
Binding sitei622 – 62212-oxoglutarate By similarity
Metal bindingi661 – 6611Magnesium By similarity
Metal bindingi694 – 6941Magnesium By similarity
Metal bindingi696 – 6961Magnesium; via carbonyl oxygen By similarity
Binding sitei968 – 9681Thiamine pyrophosphate By similarity
Binding sitei1036 – 103612-oxoglutarate By similarity
Binding sitei1054 – 10541Allosteric activator By similarity
Binding sitei1070 – 10701Allosteric activator By similarity
Binding sitei1158 – 11581Allosteric activator By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. tricarboxylic acid cycle Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Decarboxylase, Lyase, Oxidoreductase, Transferase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciMVAN350058:GIWR-4517-MONOMER.
UniPathwayiUPA00223; UER00997.
UPA00223; UER01001.

Names & Taxonomyi

Protein namesi
Recommended name:
Multifunctional 2-oxoglutarate metabolism enzyme
Alternative name(s):
2-hydroxy-3-oxoadipate synthase (EC:2.2.1.5)
Short name:
HOA synthase
Short name:
HOAS
2-oxoglutarate carboxy-lyase
2-oxoglutarate decarboxylase
Alpha-ketoglutarate decarboxylase (EC:4.1.1.71)
Short name:
KG decarboxylase
Short name:
KGD
Alpha-ketoglutarate-glyoxylate carboligase
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:kgd
Ordered Locus Names:Mvan_4477
OrganismiMycobacterium vanbaalenii (strain DSM 7251 / PYR-1)
Taxonomic identifieri350058 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000009159: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12431243Multifunctional 2-oxoglutarate metabolism enzymePRO_0000310725Add
BLAST

Interactioni

Subunit structurei

Homodimer. The 2-oxoglutarate dehydrogenase (ODH) complex contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) By similarity.

Protein-protein interaction databases

STRINGi350058.Mvan_4477.

Structurei

3D structure databases

ProteinModelPortaliA1TDK2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 40402-oxoglutarate dehydrogenase E1, N-terminal partAdd
BLAST
Regioni41 – 10363LinkerAdd
BLAST
Regioni104 – 353250Succinyltransferase E2Add
BLAST
Regioni354 – 12438902-oxoglutarate dehydrogenase E1, C-terminal partAdd
BLAST
Regioni557 – 5582Thiamine pyrophosphate binding By similarity
Regioni622 – 6243Thiamine pyrophosphate binding By similarity
Regioni661 – 6633Thiamine pyrophosphate binding By similarity
Regioni1105 – 11084Allosteric activator By similarity
Regioni1165 – 11662Allosteric activator By similarity

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili799 – 83133 Reviewed predictionAdd
BLAST

Domaini

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 By similarity.

Sequence similaritiesi

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiCOG0508.
HOGENOMiHOG000259587.
KOiK01616.
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.

A1TDK2-1 [UniParc]FASTAAdd to Basket

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MNSPSPFGQN EWLVEEMYRK FREDPSSVDP SWHEFLVDYS PEPTNDAPAG     50
NGKPAAAPTA PPEPASAPAP KPASTNGGAP PAKADTSTTR APEKKPEEKT 100
SPAPKAKTAA PAGVSDDDET QVLRGAAAAV VKNMSASLDV PTATSVRAIP 150
AKAMIDNRIV INNHLKRTRG GKISFTHLLG YAIVQAVKKF PNMNRHFAEI 200
DGKPVAVTPA HTNLGLAIDL PGKDGKRSLV VAAIKNCETM HFGQFIAAYE 250
DIVRRARDGK LTAEDFAGVT ISLTNPGTIG TVHSVPRLMK GQGAIVGAGA 300
MEYPAEFQGA SEERIAELGV GKLMTLTSTY DHRIIQGAES GDFLRTIHTL 350
LLDDEFYDEI FRELGIPHEP VRWRIDNPDS IEDKNARVIE LIAAYRNRGH 400
LMADIDPLRL DKTRFRSHPD LDVNTHGLTL WDLDREFKVN GFAGKTHKKL 450
RDILGLLRDA YCRHIGVEYT HILEPEQQQW LQERIEVKHE KPTVAEQKYI 500
LSKLNAAEAF ETFLQTKYVG QKRFSLEGAE TVIPMMDAAI DQCAEHGLDE 550
VVIGMPHRGR LNVLANIVGK PYSQIFTEFE GNLNPSQAHG SGDVKYHLGA 600
NGTYIQMFGD NDIDVSLVAN PSHLEAVDPV LEGLVRAKQD ILDKGNGPDG 650
FTVVPMMLHG DAAFAGQGVV AETLNLALLR GYRTGGTIHI IVNNQIGFTT 700
SPYDSRSSEY CTDVAKMIGA PIFHVNGDDP EACVWVAKLA VDFRQKFKKD 750
VVIDMLCYRR RGHNEGDDPS MTQPTMYDVI DTKRGVRKSY TEALIGRGDI 800
SMKEAEDALR DYQGQLERVF NEVRELEKHA IAPSSSVESD QMVPAGMSTA 850
VDKSLLARIG DAHLGYPDDF NVHPRVKPVL EKRREMAYEG KVDWAFAELL 900
ALGTFLAEGK TIRFTGQDTR RGTFTQRHSV IIDRQTGREF TPLDLLTVDS 950
DGNPTGGKFM AYDSALSEFA AVGFEYGYSV GNPNALVLWE AQFGDFVNGA 1000
QSIIDEFISS GEAKWGQLSD VVLLLPHGHE GQGPDHTSGR IERFLLLWAE 1050
GSMTIAMPST PANYFHLLRR HGLDGIHRPL IVFTPKSMLR NKAAVSDLKD 1100
FTEMKFRSVL EEPTYTEGTG DRSKAKRILL TSGKLYYELA ARKSKEGRDD 1150
VAILRLEQLA PLPKRRLAAT LDEYPNAEQY FWVQEEPANQ GAWPTLGLTL 1200
PEVLPEKLAG IKRISRRAMS APSSGSSKVH AVEQQEIIDE AFG 1243
Length:1,243
Mass (Da):136,980
Last modified:November 13, 2007 - v2
Checksum:i88066C7C78C4835D
GO

Sequence cautioni

The sequence ABM15252.1 differs from that shown. Reason: Erroneous initiation.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000511 Genomic DNA. Translation: ABM15252.1. Different initiation.
RefSeqiYP_955258.1. NC_008726.1.

Genome annotation databases

EnsemblBacteriaiABM15252; ABM15252; Mvan_4477.
GeneIDi4649093.
KEGGimva:Mvan_4477.
PATRICi18187301. VBIMycVan31953_4554.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000511 Genomic DNA. Translation: ABM15252.1 . Different initiation.
RefSeqi YP_955258.1. NC_008726.1.

3D structure databases

ProteinModelPortali A1TDK2.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 350058.Mvan_4477.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABM15252 ; ABM15252 ; Mvan_4477 .
GeneIDi 4649093.
KEGGi mva:Mvan_4477.
PATRICi 18187301. VBIMycVan31953_4554.

Phylogenomic databases

eggNOGi COG0508.
HOGENOMi HOG000259587.
KOi K01616.
OrthoDBi EOG6V1M1F.

Enzyme and pathway databases

UniPathwayi UPA00223 ; UER00997 .
UPA00223 ; UER01001 .
BioCyci MVAN350058:GIWR-4517-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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 7251 / PYR-1.

Entry informationi

Entry nameiKGD_MYCVP
AccessioniPrimary (citable) accession number: A1TDK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: November 13, 2007
Last modified: June 11, 2014
This is version 55 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

Allosteric enzyme, Complete proteome, Multifunctional enzyme

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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