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A1TDK2 (KGD_MYCVP) Reviewed, UniProtKB/Swiss-Prot

Last modified November 13, 2013. Version 53. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Multifunctional 2-oxoglutarate metabolism enzyme
Alternative name(s):
2-hydroxy-3-oxoadipate synthase
Short name=HOA synthase
Short name=HOAS
EC=2.2.1.5
2-oxoglutarate carboxy-lyase
2-oxoglutarate decarboxylase
Alpha-ketoglutarate decarboxylase
Short name=KG decarboxylase
Short name=KGD
EC=4.1.1.71
Alpha-ketoglutarate-glyoxylate carboligase

Including the following 2 domains:

  1. 2-oxoglutarate dehydrogenase E1 component
    Short name=ODH E1 component
    EC=1.2.4.2
    Alternative name(s):
    Alpha-ketoglutarate dehydrogenase E1 component
    Short name=KDH E1 component
  2. 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 names
Name:kgd
Ordered Locus Names:Mvan_4477
OrganismMycobacterium vanbaalenii (strain DSM 7251 / PYR-1) [Complete proteome] [HAMAP]
Taxonomic identifier350058 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

Protein attributes

Sequence length1243 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 activity

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.

Cofactor

Magnesium By similarity.

Thiamine pyrophosphate By similarity.

Enzyme regulation

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.

Pathway

Carbohydrate metabolism; tricarboxylic acid cycle; succinate from 2-oxoglutarate (transferase route): step 1/2.

Carbohydrate metabolism; tricarboxylic acid cycle; succinyl-CoA from 2-oxoglutarate (dehydrogenase route): step 1/1.

Subunit structure

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.

Domain

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 similarities

Belongs to the 2-oxoacid dehydrogenase family. Kgd subfamily.

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12431243Multifunctional 2-oxoglutarate metabolism enzyme
PRO_0000310725

Regions

Region1 – 40402-oxoglutarate dehydrogenase E1, N-terminal part
Region41 – 10363Linker
Region104 – 353250Succinyltransferase E2
Region354 – 12438902-oxoglutarate dehydrogenase E1, C-terminal part
Region557 – 5582Thiamine pyrophosphate binding By similarity
Region622 – 6243Thiamine pyrophosphate binding By similarity
Region661 – 6633Thiamine pyrophosphate binding By similarity
Region1105 – 11084Allosteric activator By similarity
Region1165 – 11662Allosteric activator By similarity
Coiled coil799 – 83133 Potential

Sites

Active site3321Proton acceptor; for succinyltransferase activity By similarity
Metal binding6611Magnesium By similarity
Metal binding6941Magnesium By similarity
Metal binding6961Magnesium; via carbonyl oxygen By similarity
Binding site59712-oxoglutarate By similarity
Binding site62212-oxoglutarate By similarity
Binding site9681Thiamine pyrophosphate By similarity
Binding site103612-oxoglutarate By similarity
Binding site10541Allosteric activator By similarity
Binding site10701Allosteric activator By similarity
Binding site11581Allosteric activator By similarity

Sequences

Sequence LengthMass (Da)Tools
A1TDK2 [UniParc].

Last modified November 13, 2007. Version 2.
Checksum: 88066C7C78C4835D

FASTA1,243136,980
        10         20         30         40         50         60 
MNSPSPFGQN EWLVEEMYRK FREDPSSVDP SWHEFLVDYS PEPTNDAPAG NGKPAAAPTA 

        70         80         90        100        110        120 
PPEPASAPAP KPASTNGGAP PAKADTSTTR APEKKPEEKT SPAPKAKTAA PAGVSDDDET 

       130        140        150        160        170        180 
QVLRGAAAAV VKNMSASLDV PTATSVRAIP AKAMIDNRIV INNHLKRTRG GKISFTHLLG 

       190        200        210        220        230        240 
YAIVQAVKKF PNMNRHFAEI DGKPVAVTPA HTNLGLAIDL PGKDGKRSLV VAAIKNCETM 

       250        260        270        280        290        300 
HFGQFIAAYE DIVRRARDGK LTAEDFAGVT ISLTNPGTIG TVHSVPRLMK GQGAIVGAGA 

       310        320        330        340        350        360 
MEYPAEFQGA SEERIAELGV GKLMTLTSTY DHRIIQGAES GDFLRTIHTL LLDDEFYDEI 

       370        380        390        400        410        420 
FRELGIPHEP VRWRIDNPDS IEDKNARVIE LIAAYRNRGH LMADIDPLRL DKTRFRSHPD 

       430        440        450        460        470        480 
LDVNTHGLTL WDLDREFKVN GFAGKTHKKL RDILGLLRDA YCRHIGVEYT HILEPEQQQW 

       490        500        510        520        530        540 
LQERIEVKHE KPTVAEQKYI LSKLNAAEAF ETFLQTKYVG QKRFSLEGAE TVIPMMDAAI 

       550        560        570        580        590        600 
DQCAEHGLDE VVIGMPHRGR LNVLANIVGK PYSQIFTEFE GNLNPSQAHG SGDVKYHLGA 

       610        620        630        640        650        660 
NGTYIQMFGD NDIDVSLVAN PSHLEAVDPV LEGLVRAKQD ILDKGNGPDG FTVVPMMLHG 

       670        680        690        700        710        720 
DAAFAGQGVV AETLNLALLR GYRTGGTIHI IVNNQIGFTT SPYDSRSSEY CTDVAKMIGA 

       730        740        750        760        770        780 
PIFHVNGDDP EACVWVAKLA VDFRQKFKKD VVIDMLCYRR RGHNEGDDPS MTQPTMYDVI 

       790        800        810        820        830        840 
DTKRGVRKSY TEALIGRGDI SMKEAEDALR DYQGQLERVF NEVRELEKHA IAPSSSVESD 

       850        860        870        880        890        900 
QMVPAGMSTA VDKSLLARIG DAHLGYPDDF NVHPRVKPVL EKRREMAYEG KVDWAFAELL 

       910        920        930        940        950        960 
ALGTFLAEGK TIRFTGQDTR RGTFTQRHSV IIDRQTGREF TPLDLLTVDS DGNPTGGKFM 

       970        980        990       1000       1010       1020 
AYDSALSEFA AVGFEYGYSV GNPNALVLWE AQFGDFVNGA QSIIDEFISS GEAKWGQLSD 

      1030       1040       1050       1060       1070       1080 
VVLLLPHGHE GQGPDHTSGR IERFLLLWAE GSMTIAMPST PANYFHLLRR HGLDGIHRPL 

      1090       1100       1110       1120       1130       1140 
IVFTPKSMLR NKAAVSDLKD FTEMKFRSVL EEPTYTEGTG DRSKAKRILL TSGKLYYELA 

      1150       1160       1170       1180       1190       1200 
ARKSKEGRDD VAILRLEQLA PLPKRRLAAT LDEYPNAEQY FWVQEEPANQ GAWPTLGLTL 

      1210       1220       1230       1240 
PEVLPEKLAG IKRISRRAMS APSSGSSKVH AVEQQEIIDE AFG 

« Hide

References

[1]"Complete sequence of Mycobacterium vanbaalenii PYR-1."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Singan V., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Anderson I.J., Miller C., Richardson P.
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 7251 / PYR-1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000511 Genomic DNA. Translation: ABM15252.1. Different initiation.
RefSeqYP_955258.1. NC_008726.1.

3D structure databases

ProteinModelPortalA1TDK2.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING350058.Mvan_4477.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABM15252; ABM15252; Mvan_4477.
GeneID4649093.
KEGGmva:Mvan_4477.
PATRIC18187301. VBIMycVan31953_4554.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0508.
HOGENOMHOG000259587.
KOK01616.
OrthoDBEOG6V1M1F.
ProtClustDBPRK12270.

Enzyme and pathway databases

BioCycMVAN350058:GIWR-4517-MONOMER.
UniPathwayUPA00223; UER00997.
UPA00223; UER01001.

Family and domain databases

Gene3D3.30.559.10. 1 hit.
InterProIPR001078. 2-oxoacid_DH_actylTfrase.
IPR011603. 2oxoglutarate_DH_E1.
IPR023213. CAT-like_dom.
IPR001017. DH_E1.
IPR005475. Transketolase-like_Pyr-bd.
[Graphical view]
PANTHERPTHR23152. PTHR23152. 1 hit.
PfamPF00198. 2-oxoacid_dh. 1 hit.
PF00676. E1_dh. 1 hit.
PF02779. Transket_pyr. 1 hit.
[Graphical view]
PIRSFPIRSF000157. Oxoglu_dh_E1. 1 hit.
SMARTSM00861. Transket_pyr. 1 hit.
[Graphical view]
TIGRFAMsTIGR00239. 2oxo_dh_E1. 1 hit.
ProtoNetSearch...

Entry information

Entry nameKGD_MYCVP
AccessionPrimary (citable) accession number: A1TDK2
Entry history
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: November 13, 2007
Last modified: November 13, 2013
This is version 53 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways