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A1TDK2

- KGD_MYCVP

UniProt

A1TDK2 - KGD_MYCVP

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Protein

Multifunctional 2-oxoglutarate metabolism enzyme

Gene

kgd

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).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

Protein has several cofactor binding sites:

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 activityBy similarity
Binding sitei597 – 59712-oxoglutarateBy similarity
Binding sitei622 – 62212-oxoglutarateBy similarity
Metal bindingi661 – 6611MagnesiumBy similarity
Metal bindingi694 – 6941MagnesiumBy similarity
Metal bindingi696 – 6961Magnesium; via carbonyl oxygenBy similarity
Binding sitei968 – 9681Thiamine pyrophosphateBy similarity
Binding sitei1036 – 103612-oxoglutarateBy similarity
Binding sitei1054 – 10541Allosteric activatorBy similarity
Binding sitei1070 – 10701Allosteric activatorBy similarity
Binding sitei1158 – 11581Allosteric 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

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).By similarity

Protein-protein interaction databases

STRINGi350058.Mvan_4477.

Structurei

3D structure databases

ProteinModelPortaliA1TDK2.
ModBaseiSearch...
MobiDBiSearch...

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 bindingBy similarity
Regioni622 – 6243Thiamine pyrophosphate bindingBy similarity
Regioni661 – 6633Thiamine pyrophosphate bindingBy similarity
Regioni1105 – 11084Allosteric activatorBy similarity
Regioni1165 – 11662Allosteric activatorBy similarity

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili799 – 83133Sequence AnalysisAdd
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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        10         20         30         40         50
MNSPSPFGQN EWLVEEMYRK FREDPSSVDP SWHEFLVDYS PEPTNDAPAG
60 70 80 90 100
NGKPAAAPTA PPEPASAPAP KPASTNGGAP PAKADTSTTR APEKKPEEKT
110 120 130 140 150
SPAPKAKTAA PAGVSDDDET QVLRGAAAAV VKNMSASLDV PTATSVRAIP
160 170 180 190 200
AKAMIDNRIV INNHLKRTRG GKISFTHLLG YAIVQAVKKF PNMNRHFAEI
210 220 230 240 250
DGKPVAVTPA HTNLGLAIDL PGKDGKRSLV VAAIKNCETM HFGQFIAAYE
260 270 280 290 300
DIVRRARDGK LTAEDFAGVT ISLTNPGTIG TVHSVPRLMK GQGAIVGAGA
310 320 330 340 350
MEYPAEFQGA SEERIAELGV GKLMTLTSTY DHRIIQGAES GDFLRTIHTL
360 370 380 390 400
LLDDEFYDEI FRELGIPHEP VRWRIDNPDS IEDKNARVIE LIAAYRNRGH
410 420 430 440 450
LMADIDPLRL DKTRFRSHPD LDVNTHGLTL WDLDREFKVN GFAGKTHKKL
460 470 480 490 500
RDILGLLRDA YCRHIGVEYT HILEPEQQQW LQERIEVKHE KPTVAEQKYI
510 520 530 540 550
LSKLNAAEAF ETFLQTKYVG QKRFSLEGAE TVIPMMDAAI DQCAEHGLDE
560 570 580 590 600
VVIGMPHRGR LNVLANIVGK PYSQIFTEFE GNLNPSQAHG SGDVKYHLGA
610 620 630 640 650
NGTYIQMFGD NDIDVSLVAN PSHLEAVDPV LEGLVRAKQD ILDKGNGPDG
660 670 680 690 700
FTVVPMMLHG DAAFAGQGVV AETLNLALLR GYRTGGTIHI IVNNQIGFTT
710 720 730 740 750
SPYDSRSSEY CTDVAKMIGA PIFHVNGDDP EACVWVAKLA VDFRQKFKKD
760 770 780 790 800
VVIDMLCYRR RGHNEGDDPS MTQPTMYDVI DTKRGVRKSY TEALIGRGDI
810 820 830 840 850
SMKEAEDALR DYQGQLERVF NEVRELEKHA IAPSSSVESD QMVPAGMSTA
860 870 880 890 900
VDKSLLARIG DAHLGYPDDF NVHPRVKPVL EKRREMAYEG KVDWAFAELL
910 920 930 940 950
ALGTFLAEGK TIRFTGQDTR RGTFTQRHSV IIDRQTGREF TPLDLLTVDS
960 970 980 990 1000
DGNPTGGKFM AYDSALSEFA AVGFEYGYSV GNPNALVLWE AQFGDFVNGA
1010 1020 1030 1040 1050
QSIIDEFISS GEAKWGQLSD VVLLLPHGHE GQGPDHTSGR IERFLLLWAE
1060 1070 1080 1090 1100
GSMTIAMPST PANYFHLLRR HGLDGIHRPL IVFTPKSMLR NKAAVSDLKD
1110 1120 1130 1140 1150
FTEMKFRSVL EEPTYTEGTG DRSKAKRILL TSGKLYYELA ARKSKEGRDD
1160 1170 1180 1190 1200
VAILRLEQLA PLPKRRLAAT LDEYPNAEQY FWVQEEPANQ GAWPTLGLTL
1210 1220 1230 1240
PEVLPEKLAG IKRISRRAMS APSSGSSKVH AVEQQEIIDE AFG
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. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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: November 26, 2014
This is version 57 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, Reference proteome

Documents

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

External Data

Dasty 3