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Protein

Multifunctional 2-oxoglutarate metabolism enzyme

Gene

kgd

Organism
Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)
Status
Reviewed-Annotation score: 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

Pathway: tricarboxylic acid cycle

This protein is involved in step 1 of the subpathway that synthesizes succinate from 2-oxoglutarate (transferase route).
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Multifunctional 2-oxoglutarate metabolism enzyme (kgd)
  2. no protein annotated in this organism
This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes succinate from 2-oxoglutarate (transferase route), the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

Pathway: tricarboxylic acid cycle

This protein is involved in step 1 of the subpathway that synthesizes succinyl-CoA from 2-oxoglutarate (dehydrogenase route).
Proteins known to be involved in this subpathway in this organism are:
  1. Multifunctional 2-oxoglutarate metabolism enzyme (kgd)
This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes succinyl-CoA from 2-oxoglutarate (dehydrogenase route), the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

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 bindingi665 – 6651MagnesiumBy similarity
Metal bindingi698 – 6981MagnesiumBy similarity
Metal bindingi700 – 7001Magnesium; via carbonyl oxygenBy similarity
Binding sitei972 – 9721Thiamine pyrophosphateBy similarity
Binding sitei1040 – 104012-oxoglutarateBy similarity
Binding sitei1058 – 10581Allosteric activatorBy similarity
Binding sitei1074 – 10741Allosteric activatorBy similarity
Binding sitei1162 – 11621Allosteric activatorBy similarity

GO - Molecular functioni

GO - Biological processi

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

BioCyciMAVI262316:GCQR-2572-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:MAP_2536
OrganismiMycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)
Taxonomic identifieri262316 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium avium complex (MAC)
ProteomesiUP000000580 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12471247Multifunctional 2-oxoglutarate metabolism enzymePRO_0000310717Add
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

STRINGi262316.MAP2536.

Structurei

3D structure databases

ProteinModelPortaliQ73WX4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 41412-oxoglutarate dehydrogenase E1, N-terminal partAdd
BLAST
Regioni42 – 10463LinkerAdd
BLAST
Regioni105 – 353249Succinyltransferase E2Add
BLAST
Regioni354 – 12478942-oxoglutarate dehydrogenase E1, C-terminal partAdd
BLAST
Regioni557 – 5582Thiamine pyrophosphate bindingBy similarity
Regioni622 – 6243Thiamine pyrophosphate bindingBy similarity
Regioni665 – 6673Thiamine pyrophosphate bindingBy similarity
Regioni1109 – 11124Allosteric activatorBy similarity
Regioni1169 – 11702Allosteric activatorBy similarity

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili803 – 83331Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi51 – 12979Ala-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.
KOiK01616.
OMAiQNQGAWF.
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.

Q73WX4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNISSPFGQ NEWLVEEMYR KFRDDPSSVD PSWHEFLVDY NPEPTGDSVL
60 70 80 90 100
AAPASTDGPS APAPAAPQTA QPALPAQTAP PAQTAQPARP APQPAAAPGN
110 120 130 140 150
GASTRPAKPA TPPPAEGDEL QTLRGAAAAV VKNMSASLEV PTATSVRAIP
160 170 180 190 200
AKLLIDNRIV INNQLKRTRG GKISFTHLLG YALVQAIKKF PNMNRHYAEI
210 220 230 240 250
DGKPTAITPA HTNLGLAIDL QGKDGKRSLV VAGIKNCETM RFAQFVTAYE
260 270 280 290 300
DIVRRARDGK LTAEDFAGVT ISLTNPGTIG TVHSVPRLMN GQGAIIGVGA
310 320 330 340 350
MEYPAEFQGA SEERIAELGI GKLITLTSTY DHRIIQGAES GDFLRTIHEM
360 370 380 390 400
LLSDGFWDDI FRELSIPYLP IRWSTDNPDS IVDKNARVME LIAAYRNRGH
410 420 430 440 450
LMADIDPLRL DGSRFRSHPD LEILNHGLTL WDLDRVFKVN GFAGAEYKKL
460 470 480 490 500
RDILGLLRDA YCRHIGVEYT HILDPEQQEW LQQRVETKHV KPTVAEQKFI
510 520 530 540 550
LSKLNAAEAF ETFLQTKYVG QKRFSLEGAE SVIPMMDAAI DQCAEHGLDE
560 570 580 590 600
VVIGMPHRGR LNVLANIVGK PYSQIFSEFE GNLNPAQAHG SGDVKYHLGA
610 620 630 640 650
TGVYLQMFGD NDIQVSLTAN PSHLEAVDPV LEGLVRAKQD LLDHGADDQG
660 670 680 690 700
DEKAFSVVPM MLHGDAAFAG QGVVAETLNL THLPGYRVGG TIHIIVNNQI
710 720 730 740 750
GFTTAPEHSR SSEYCTDVAK MIGAPIFHVN GDDPEACAWV AKLAVDFRQK
760 770 780 790 800
FKKDVVIDML CYRKRGHNEG DDPSMTNPAM YDVVDIKRGV RKSYTEALIG
810 820 830 840 850
RGDISMKEAE DALRDYQGQL ERVFNEVREL EKHGVGPSES VEADQMLPAG
860 870 880 890 900
LATAVDKALL ARIGDAFLAL PEGFTAHPRV QPVLEKRREM AYEGKIDWAF
910 920 930 940 950
AELLALGSLV AGGKLVRLSG QDTRRGTFSQ RHSVIIDRNT GEEFTPLQLL
960 970 980 990 1000
ATNPDGTPTG GKFLVYDSPL SEYAAVGFEY GYTVGNPDAL VLWEAQFGDF
1010 1020 1030 1040 1050
VNGAQSIIDE FISSGEAKWG QLSNVVLLLP HGHEGQGPDH TSARIERFLQ
1060 1070 1080 1090 1100
LWAEGSMTIA MPSTPSNYFH LLRRHALDGI KRPLIVFTPK SMLRNKAAVS
1110 1120 1130 1140 1150
DIKDFTEIKF RSVLEEPTYE DGIGDRGKVS RVLLTSGKLY YELVARKNKD
1160 1170 1180 1190 1200
NRDDVAIVRI EQLAPLPKRR LGETLDRYPN VREYFWVQEE PANQGAWPRF
1210 1220 1230 1240
GLELPELLPD KLTGLKRISR RAMSAPSSGS SKVHAVEQQE IIDTAFA
Length:1,247
Mass (Da):137,073
Last modified:July 5, 2004 - v1
Checksum:iD31E9876D146519A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016958 Genomic DNA. Translation: AAS04853.1.
RefSeqiNP_961470.1. NC_002944.2.
WP_010949638.1. NC_002944.2.

Genome annotation databases

EnsemblBacteriaiAAS04853; AAS04853; MAP_2536.
GeneIDi2719042.
KEGGimpa:MAP2536.
PATRICi17997756. VBIMycAvi108102_2692.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016958 Genomic DNA. Translation: AAS04853.1.
RefSeqiNP_961470.1. NC_002944.2.
WP_010949638.1. NC_002944.2.

3D structure databases

ProteinModelPortaliQ73WX4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi262316.MAP2536.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS04853; AAS04853; MAP_2536.
GeneIDi2719042.
KEGGimpa:MAP2536.
PATRICi17997756. VBIMycAvi108102_2692.

Phylogenomic databases

eggNOGiCOG0508.
KOiK01616.
OMAiQNQGAWF.
OrthoDBiEOG6V1M1F.

Enzyme and pathway databases

UniPathwayiUPA00223; UER00997.
UPA00223; UER01001.
BioCyciMAVI262316:GCQR-2572-MONOMER.

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.
ProtoNetiSearch...

Publicationsi

  1. "The complete genome sequence of Mycobacterium avium subspecies paratuberculosis."
    Li L., Bannantine J.P., Zhang Q., Amonsin A., May B.J., Alt D., Banerji N., Kanjilal S., Kapur V.
    Proc. Natl. Acad. Sci. U.S.A. 102:12344-12349(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-968 / K-10.

Entry informationi

Entry nameiKGD_MYCPA
AccessioniPrimary (citable) accession number: Q73WX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: July 5, 2004
Last modified: June 24, 2015
This is version 81 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, 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.