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A0PVU7

- KGD_MYCUA

UniProt

A0PVU7 - KGD_MYCUA

Protein

Multifunctional 2-oxoglutarate metabolism enzyme

Gene

kgd

Organism
Mycobacterium ulcerans (strain Agy99)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 58 (01 Oct 2014)
      Sequence version 1 (09 Jan 2007)
      Previous versions | rss
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    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.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 sitei322 – 3221Proton acceptor; for succinyltransferase activityBy similarity
    Binding sitei588 – 58812-oxoglutarateBy similarity
    Binding sitei613 – 61312-oxoglutarateBy similarity
    Metal bindingi656 – 6561MagnesiumBy similarity
    Metal bindingi689 – 6891MagnesiumBy similarity
    Metal bindingi691 – 6911Magnesium; via carbonyl oxygenBy similarity
    Binding sitei963 – 9631Thiamine pyrophosphateBy similarity
    Binding sitei1031 – 103112-oxoglutarateBy similarity
    Binding sitei1049 – 10491Allosteric activatorBy similarity
    Binding sitei1065 – 10651Allosteric activatorBy similarity
    Binding sitei1153 – 11531Allosteric activatorBy 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

    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

    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:MUL_4500
    OrganismiMycobacterium ulcerans (strain Agy99)
    Taxonomic identifieri362242 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
    ProteomesiUP000000765: Chromosome

    Organism-specific databases

    GenoListiMUL_4500.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12381238Multifunctional 2-oxoglutarate metabolism enzymePRO_0000310724Add
    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.By similarity

    Protein-protein interaction databases

    STRINGi362242.MUL_4500.

    Structurei

    3D structure databases

    ProteinModelPortaliA0PVU7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 41412-oxoglutarate dehydrogenase E1, N-terminal partAdd
    BLAST
    Regioni42 – 9453LinkerAdd
    BLAST
    Regioni95 – 343249Succinyltransferase E2Add
    BLAST
    Regioni344 – 12388952-oxoglutarate dehydrogenase E1, C-terminal partAdd
    BLAST
    Regioni548 – 5492Thiamine pyrophosphate bindingBy similarity
    Regioni613 – 6153Thiamine pyrophosphate bindingBy similarity
    Regioni656 – 6583Thiamine pyrophosphate bindingBy similarity
    Regioni1100 – 11034Allosteric activatorBy similarity
    Regioni1160 – 11612Allosteric activatorBy similarity

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili794 – 82431Sequence AnalysisAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi48 – 11972Ala-richAdd
    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.
    OMAiDPLEYKQ.
    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.

    A0PVU7-1 [UniParc]FASTAAdd to Basket

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    MANISSPFGQ NEWLVEEMYR KFRDDPSSVD PSWHEFLVDY NPESTQEATE     50
    PAVVKPAAAP AKPAPAPAPA KPAAGPPAAG NGSPAAAPSA KPAAAPAKAP 100
    APPPAEGDEM QVLRGAAAAV VKNMSASLDV PTATSVRAVP AKLLIDNRIV 150
    INNQLKRNRG GKISFTHLLG YALVQAVKKF PNMNRHYLDV DGKPNAVTPA 200
    HTNLGLAIDL QGKDGKRALV VAGIKRCETM RFAQFVTAYE DIVRRARDGK 250
    LTAEDFSGVT ISLTNPGTIG TVHSVPRLMA GQGAIIGVGA MEYPAEFQGA 300
    SEERIAELGI GKLITLTSTY DHRIIQGAES GDFLRTIHQM LLADEFWDEI 350
    FRELSIPYLP VRWRPDNPDS IVDKNARIIE LIAAYRNRGH LMADIDPLRL 400
    DKTRFRSHPD LDVCTHGLTL WDLDRSFKVG GCFAGPQNMK LRDVLSILRD 450
    TYCRHVGVEY THILEPEQQQ WLQQRVEAKH VKPTVAQQKY VLSKLNAAEA 500
    FETFLQTKYV GQKRFSLEGA ESVIPMMDAA IDQCAEYGLD EVVIGMPHRG 550
    RLNVLANIVG KPYSQIFSEF EGNLNPSQAH GSGDVKYHLG ATGVYLQMFG 600
    DNDIQVSLTA NPSHLEAVDP VLEGLVRAKQ DLLEHGETDT ENQRAFSVVP 650
    MMLHGDAAFA GQGVVAETLN LANLPGYRVG GTIHIIVNNQ IGFTTAPEYS 700
    RSTEYCTDVA KTIGAPIFHV NGDDPEACVW VARLAVDFRQ RFNKDVIIDM 750
    LCYRRRGHNE GDDPSMTNPR MYDVVDTKRG VRKSYTEALI GRGDISIKEA 800
    EDALRDYQGQ LEQVFNEVRE LEKHGAQPSE SVESDQMIPA GLATAVDKSL 850
    LARIGDAFLA VPDGFTTHPR VQPVLEKRRE MAYEGKIDWA FAELLALGSL 900
    VAEGKLVRFS GQDTRRGTFS QRHSVIIDRH TREEFTPLQL LTTNKDGSPT 950
    GGKFLVYDSP LSEYAAVGFE YGYTVGNPDA VVLWEAQFGD FVNGAQSIID 1000
    EFISSGEAKW GQLSNVVLLL PHGHEGQGPD HTSGRIERFL QLWAEGSMTI 1050
    AMPSTPSNYF HLLRRHALDG IQRPLIVFTP KSMLRNKAAV SDIKDFTEIK 1100
    FRSVLEEPTY EDGVGDRNLV NRILLTSGKI YYEMVARKAK DKREDVAIVR 1150
    VEQLAPLPRR RLRETLDRYP NAKEFFWVQE EPANQGAWPR FGLELPELLP 1200
    EKLSGVKRIS RRAMSAPSSG SSKVHAVEQQ EILDTAFG 1238
    Length:1,238
    Mass (Da):136,742
    Last modified:January 9, 2007 - v1
    Checksum:iB9A7DB3108194D2A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000325 Genomic DNA. Translation: ABL06466.1.
    RefSeqiYP_907937.1. NC_008611.1.

    Genome annotation databases

    EnsemblBacteriaiABL06466; ABL06466; MUL_4500.
    GeneIDi4549927.
    KEGGimul:MUL_4500.
    PATRICi18176818. VBIMycUlc37413_5210.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000325 Genomic DNA. Translation: ABL06466.1 .
    RefSeqi YP_907937.1. NC_008611.1.

    3D structure databases

    ProteinModelPortali A0PVU7.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 362242.MUL_4500.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABL06466 ; ABL06466 ; MUL_4500 .
    GeneIDi 4549927.
    KEGGi mul:MUL_4500.
    PATRICi 18176818. VBIMycUlc37413_5210.

    Organism-specific databases

    GenoListi MUL_4500.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00223 ; UER00997 .
    UPA00223 ; UER01001 .

    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. "Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer."
      Stinear T.P., Seemann T., Pidot S., Frigui W., Reysset G., Garnier T., Meurice G., Simon D., Bouchier C., Ma L., Tichit M., Porter J.L., Ryan J., Johnson P.D.R., Davies J.K., Jenkin G.A., Small P.L.C., Jones L.M.
      , Tekaia F., Laval F., Daffe M., Parkhill J., Cole S.T.
      Genome Res. 17:192-200(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Agy99.

    Entry informationi

    Entry nameiKGD_MYCUA
    AccessioniPrimary (citable) accession number: A0PVU7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 13, 2007
    Last sequence update: January 9, 2007
    Last modified: October 1, 2014
    This is version 58 of the entry and version 1 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