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A0PVU7

- KGD_MYCUA

UniProt

A0PVU7 - KGD_MYCUA

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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

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
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

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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        10         20         30         40         50
MANISSPFGQ NEWLVEEMYR KFRDDPSSVD PSWHEFLVDY NPESTQEATE
60 70 80 90 100
PAVVKPAAAP AKPAPAPAPA KPAAGPPAAG NGSPAAAPSA KPAAAPAKAP
110 120 130 140 150
APPPAEGDEM QVLRGAAAAV VKNMSASLDV PTATSVRAVP AKLLIDNRIV
160 170 180 190 200
INNQLKRNRG GKISFTHLLG YALVQAVKKF PNMNRHYLDV DGKPNAVTPA
210 220 230 240 250
HTNLGLAIDL QGKDGKRALV VAGIKRCETM RFAQFVTAYE DIVRRARDGK
260 270 280 290 300
LTAEDFSGVT ISLTNPGTIG TVHSVPRLMA GQGAIIGVGA MEYPAEFQGA
310 320 330 340 350
SEERIAELGI GKLITLTSTY DHRIIQGAES GDFLRTIHQM LLADEFWDEI
360 370 380 390 400
FRELSIPYLP VRWRPDNPDS IVDKNARIIE LIAAYRNRGH LMADIDPLRL
410 420 430 440 450
DKTRFRSHPD LDVCTHGLTL WDLDRSFKVG GCFAGPQNMK LRDVLSILRD
460 470 480 490 500
TYCRHVGVEY THILEPEQQQ WLQQRVEAKH VKPTVAQQKY VLSKLNAAEA
510 520 530 540 550
FETFLQTKYV GQKRFSLEGA ESVIPMMDAA IDQCAEYGLD EVVIGMPHRG
560 570 580 590 600
RLNVLANIVG KPYSQIFSEF EGNLNPSQAH GSGDVKYHLG ATGVYLQMFG
610 620 630 640 650
DNDIQVSLTA NPSHLEAVDP VLEGLVRAKQ DLLEHGETDT ENQRAFSVVP
660 670 680 690 700
MMLHGDAAFA GQGVVAETLN LANLPGYRVG GTIHIIVNNQ IGFTTAPEYS
710 720 730 740 750
RSTEYCTDVA KTIGAPIFHV NGDDPEACVW VARLAVDFRQ RFNKDVIIDM
760 770 780 790 800
LCYRRRGHNE GDDPSMTNPR MYDVVDTKRG VRKSYTEALI GRGDISIKEA
810 820 830 840 850
EDALRDYQGQ LEQVFNEVRE LEKHGAQPSE SVESDQMIPA GLATAVDKSL
860 870 880 890 900
LARIGDAFLA VPDGFTTHPR VQPVLEKRRE MAYEGKIDWA FAELLALGSL
910 920 930 940 950
VAEGKLVRFS GQDTRRGTFS QRHSVIIDRH TREEFTPLQL LTTNKDGSPT
960 970 980 990 1000
GGKFLVYDSP LSEYAAVGFE YGYTVGNPDA VVLWEAQFGD FVNGAQSIID
1010 1020 1030 1040 1050
EFISSGEAKW GQLSNVVLLL PHGHEGQGPD HTSGRIERFL QLWAEGSMTI
1060 1070 1080 1090 1100
AMPSTPSNYF HLLRRHALDG IQRPLIVFTP KSMLRNKAAV SDIKDFTEIK
1110 1120 1130 1140 1150
FRSVLEEPTY EDGVGDRNLV NRILLTSGKI YYEMVARKAK DKREDVAIVR
1160 1170 1180 1190 1200
VEQLAPLPRR RLRETLDRYP NAKEFFWVQE EPANQGAWPR FGLELPELLP
1210 1220 1230
EKLSGVKRIS RRAMSAPSSG SSKVHAVEQQ EILDTAFG
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.
RefSeqiWP_011742065.1. NC_008611.1.
YP_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 WP_011742065.1. NC_008611.1.
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 29, 2014
This is version 59 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