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A5U1U6

- KGD_MYCTA

UniProt

A5U1U6 - KGD_MYCTA

Protein

Multifunctional 2-oxoglutarate metabolism enzyme

Gene

kgd

Organism
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 53 (01 Oct 2014)
      Sequence version 2 (13 Nov 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 sitei316 – 3161Proton acceptor; for succinyltransferase activityBy similarity
    Binding sitei581 – 58112-oxoglutarateBy similarity
    Binding sitei606 – 60612-oxoglutarateBy similarity
    Metal bindingi649 – 6491MagnesiumBy similarity
    Metal bindingi682 – 6821MagnesiumBy similarity
    Metal bindingi684 – 6841Magnesium; via carbonyl oxygenBy similarity
    Binding sitei956 – 9561Thiamine pyrophosphateBy similarity
    Binding sitei1024 – 102412-oxoglutarateBy similarity
    Binding sitei1042 – 10421Allosteric activatorBy similarity
    Binding sitei1058 – 10581Allosteric activatorBy similarity
    Binding sitei1146 – 11461Allosteric 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

    BioCyciMTUB419947:GJ8N-1295-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:MRA_1256
    OrganismiMycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
    Taxonomic identifieri419947 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
    ProteomesiUP000001988: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12311231Multifunctional 2-oxoglutarate metabolism enzymePRO_0000310723Add
    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

    STRINGi419947.MRA_1256.

    Structurei

    3D structure databases

    ProteinModelPortaliA5U1U6.
    SMRiA5U1U6. Positions 116-335, 367-1231.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 41412-oxoglutarate dehydrogenase E1, N-terminal partAdd
    BLAST
    Regioni42 – 8847LinkerAdd
    BLAST
    Regioni89 – 337249Succinyltransferase E2Add
    BLAST
    Regioni338 – 12318942-oxoglutarate dehydrogenase E1, C-terminal partAdd
    BLAST
    Regioni541 – 5422Thiamine pyrophosphate bindingBy similarity
    Regioni606 – 6083Thiamine pyrophosphate bindingBy similarity
    Regioni649 – 6513Thiamine pyrophosphate bindingBy similarity
    Regioni1093 – 10964Allosteric activatorBy similarity
    Regioni1153 – 11542Allosteric activatorBy similarity

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili787 – 81731Sequence AnalysisAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi61 – 11353Ala-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.
    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.

    A5U1U6-1 [UniParc]FASTAAdd to Basket

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    MANISSPFGQ NEWLVEEMYR KFRDDPSSVD PSWHEFLVDY SPEPTSQPAA     50
    EPTRVTSPLV AERAAAAAPQ APPKPADTAA AGNGVVAALA AKTAVPPPAE 100
    GDEVAVLRGA AAAVVKNMSA SLEVPTATSV RAVPAKLLID NRIVINNQLK 150
    RTRGGKISFT HLLGYALVQA VKKFPNMNRH YTEVDGKPTA VTPAHTNLGL 200
    AIDLQGKDGK RSLVVAGIKR CETMRFAQFV TAYEDIVRRA RDGKLTTEDF 250
    AGVTISLTNP GTIGTVHSVP RLMPGQGAII GVGAMEYPAE FQGASEERIA 300
    ELGIGKLITL TSTYDHRIIQ GAESGDFLRT IHELLLSDGF WDEVFRELSI 350
    PYLPVRWSTD NPDSIVDKNA RVMNLIAAYR NRGHLMADTD PLRLDKARFR 400
    SHPDLEVLTH GLTLWDLDRV FKVDGFAGAQ YKKLRDVLGL LRDAYCRHIG 450
    VEYAHILDPE QKEWLEQRVE TKHVKPTVAQ QKYILSKLNA AEAFETFLQT 500
    KYVGQKRFSL EGAESVIPMM DAAIDQCAEH GLDEVVIGMP HRGRLNVLAN 550
    IVGKPYSQIF TEFEGNLNPS QAHGSGDVKY HLGATGLYLQ MFGDNDIQVS 600
    LTANPSHLEA VDPVLEGLVR AKQDLLDHGS IDSDGQRAFS VVPLMLHGDA 650
    AFAGQGVVAE TLNLANLPGY RVGGTIHIIV NNQIGFTTAP EYSRSSEYCT 700
    DVAKMIGAPI FHVNGDDPEA CVWVARLAVD FRQRFKKDVV IDMLCYRRRG 750
    HNEGDDPSMT NPYVYDVVDT KRGARKSYTE ALIGRGDISM KEAEDALRDY 800
    QGQLERVFNE VRELEKHGVQ PSESVESDQM IPAGLATAVD KSLLARIGDA 850
    FLALPNGFTA HPRVQPVLEK RREMAYEGKI DWAFGELLAL GSLVAEGKLV 900
    RLSGQDSRRG TFSQRHSVLI DRHTGEEFTP LQLLATNSDG SPTGGKFLVY 950
    DSPLSEYAAV GFEYGYTVGN PDAVVLWEAQ FGDFVNGAQS IIDEFISSGE 1000
    AKWGQLSNVV LLLPHGHEGQ GPDHTSARIE RFLQLWAEGS MTIAMPSTPS 1050
    NYFHLLRRHA LDGIQRPLIV FTPKSMLRHK AAVSEIKDFT EIKFRSVLEE 1100
    PTYEDGIGDR NKVSRILLTS GKLYYELAAR KAKDNRNDLA IVRLEQLAPL 1150
    PRRRLRETLD RYENVKEFFW VQEEPANQGA WPRFGLELPE LLPDKLAGIK 1200
    RISRRAMSAP SSGSSKVHAV EQQEILDEAF G 1231
    Length:1,231
    Mass (Da):135,902
    Last modified:November 13, 2007 - v2
    Checksum:i96C255612BA12889
    GO

    Sequence cautioni

    The sequence ABQ72996.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000611 Genomic DNA. Translation: ABQ72996.1. Different initiation.
    RefSeqiYP_001282558.1. NC_009525.1.

    Genome annotation databases

    EnsemblBacteriaiABQ72996; ABQ72996; MRA_1256.
    GeneIDi5214632.
    KEGGimra:MRA_1256.
    PATRICi18142389. VBIMycTub106795_1401.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000611 Genomic DNA. Translation: ABQ72996.1 . Different initiation.
    RefSeqi YP_001282558.1. NC_009525.1.

    3D structure databases

    ProteinModelPortali A5U1U6.
    SMRi A5U1U6. Positions 116-335, 367-1231.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 419947.MRA_1256.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABQ72996 ; ABQ72996 ; MRA_1256 .
    GeneIDi 5214632.
    KEGGi mra:MRA_1256.
    PATRICi 18142389. VBIMycTub106795_1401.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00223 ; UER00997 .
    UPA00223 ; UER01001 .
    BioCyci MTUB419947:GJ8N-1295-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. "Complete genomic sequence of Mycobacterium tuberculosis strain H37Ra, a non-pathogenic variant closely related to the well-characterized pathogenic strain H37Rv."
      Wang S.Y., Zheng H.J., Lv L.D., Wang B.F., Zhang X.L., Pu S.Y., Zhu G.F., Wang H.H., Zhao G.P., Zhang Y.
      Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 25177 / H37Ra.

    Entry informationi

    Entry nameiKGD_MYCTA
    AccessioniPrimary (citable) accession number: A5U1U6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 13, 2007
    Last sequence update: November 13, 2007
    Last modified: October 1, 2014
    This is version 53 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