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Q1B4V6

- KGD_MYCSS

UniProt

Q1B4V6 - KGD_MYCSS

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Protein

Multifunctional 2-oxoglutarate metabolism enzyme

Gene

kgd

Organism
Mycobacterium sp. (strain MCS)
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 sitei357 – 3571Proton acceptor; for succinyltransferase activityBy similarity
Binding sitei622 – 62212-oxoglutarateBy similarity
Binding sitei647 – 64712-oxoglutarateBy similarity
Metal bindingi686 – 6861MagnesiumBy similarity
Metal bindingi719 – 7191MagnesiumBy similarity
Metal bindingi721 – 7211Magnesium; via carbonyl oxygenBy similarity
Binding sitei993 – 9931Thiamine pyrophosphateBy similarity
Binding sitei1061 – 106112-oxoglutarateBy similarity
Binding sitei1079 – 10791Allosteric activatorBy similarity
Binding sitei1095 – 10951Allosteric activatorBy similarity
Binding sitei1183 – 11831Allosteric 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

BioCyciMSP164756:GHQ8-4015-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:Mmcs_3973
OrganismiMycobacterium sp. (strain MCS)
Taxonomic identifieri164756 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000001972: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12691269Multifunctional 2-oxoglutarate metabolism enzymePRO_0000310721Add
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

STRINGi164756.Mmcs_3973.

Structurei

3D structure databases

ProteinModelPortaliQ1B4V6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 41412-oxoglutarate dehydrogenase E1, N-terminal partAdd
BLAST
Regioni42 – 10766LinkerAdd
BLAST
Regioni108 – 378271Succinyltransferase E2Add
BLAST
Regioni379 – 12698912-oxoglutarate dehydrogenase E1, C-terminal partAdd
BLAST
Regioni582 – 5832Thiamine pyrophosphate bindingBy similarity
Regioni647 – 6493Thiamine pyrophosphate bindingBy similarity
Regioni686 – 6883Thiamine pyrophosphate bindingBy similarity
Regioni1130 – 11334Allosteric activatorBy similarity
Regioni1190 – 11912Allosteric activatorBy similarity

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili824 – 85532Sequence 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.
OMAiGHQNANL.
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.

Q1B4V6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSSSPSPFGQ NEWLVEEMYR KFREDPSSVD PSWHEFLVDY NPEPTTDSSA
60 70 80 90 100
SENGQQTRTA APKAPPEPAP APAPKTPDSK TPDSKSQAPK QDSKPQESKP
110 120 130 140 150
QAKAKPAESK SSTKPADAKS EKSGKSGTNG AAKPAAQPAD DSDQNQVLRG
160 170 180 190 200
AAAAVAKNMS ASLDVPTATS VRAIPAKLMI DNRVVINNHL KRTRGGKISF
210 220 230 240 250
THLIGYAIVA AVKKFPNMNR HFAEVDGKPN AVTPAHTNLG LAIDLQGKDG
260 270 280 290 300
NRQLVVAAIK KADTMRFGQF IAAYEDIVRR ARDGKLTAED FSGVTISLTN
310 320 330 340 350
PGTIGTVHSV PRLMRGQGAI IGVGAMEYPA EFQGASEERI ADLGIGKLIT
360 370 380 390 400
LTSTYDHRII QGAESGDFLR TVHQLLLSDD FFDEIFRELG IPYEPVRWRT
410 420 430 440 450
DNPDSIEDKN ARVIELIAAY RNRGHLMADI DPLRLDSNRF RSHPDLDVLT
460 470 480 490 500
HGLTLWDLDR EFKVNGFAGA ERKKLRDVLA VLRDAYCRHI GVEYTHILEP
510 520 530 540 550
EQQQWLQERI EGKHEKPTVA QQKYILSRLN AAEAFETFLQ TKYVGQKRFS
560 570 580 590 600
LEGAETVIPA MDAVIDQCAE HALDEVVIGM PHRGRLNVLA NIVGKPYSQI
610 620 630 640 650
FSEFEGNLNP SQAHGSGDVK YHLGSSGTYL QMFGDNDITV SLTANPSHLE
660 670 680 690 700
AVDPVMEGLV RAKQDLLDKG DTEDGYTVVP LMLHGDAAFA GQGVVAETLN
710 720 730 740 750
LALLRGYRTG GTIHLIVNNQ IGFTTSPAAA KSSEYCTDVA KMIGAPIFHV
760 770 780 790 800
NGDDPEAAVW VSRLAVDFRQ KFKKDVVIDL LCYRRRGHNE GDDPSMTQPS
810 820 830 840 850
MYDVIDTKRG VRKSYTEALI GRGDISMKEA EDALRDYQGQ LEQVFNEVRE
860 870 880 890 900
LEKHEIEPSE SVEADQQIPA KLATAVDKSL LARIGDAHLA VPEGFTVHPR
910 920 930 940 950
VKPVLEKRRE MAYEGKVDWA FAELLALGTM ISEGKLVRLS GQDTRRGTFT
960 970 980 990 1000
QRHSVVIDRK TGKEFTPLQL LATDSDGNPT GGKFLVYDSP LSEFAAVGFE
1010 1020 1030 1040 1050
YGYSVGNPDA MVLWEAQFGD FINGAQSIID EFISSGEAKW GQLSDVVLLL
1060 1070 1080 1090 1100
PHGHEGQGPD HTSGRIERFL QLWAEGSMTI ALPSTPANYF HLLRRHSLDG
1110 1120 1130 1140 1150
IQRPLIVFTP KSMLRNKAAV SDIRDFTEQK FRSVLEEPTY TDGDGDRNKV
1160 1170 1180 1190 1200
TRILLTSGKI YYELVARKNK ESRDDVAIVR IEQLAPLPKR RLAETLDKYP
1210 1220 1230 1240 1250
NVEEKFWVQE EPANQGAWPT FGLTLPEMLP DHFTGIKRIS RRAMSAPSSG
1260
SSKVHAVEQQ EILDEAFAP
Length:1,269
Mass (Da):140,119
Last modified:July 11, 2006 - v1
Checksum:iF6F4221B80E76B83
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000384 Genomic DNA. Translation: ABG10078.1.
RefSeqiYP_641134.1. NC_008146.1.

Genome annotation databases

EnsemblBacteriaiABG10078; ABG10078; Mmcs_3973.
GeneIDi4112803.
KEGGimmc:Mmcs_3973.
PATRICi18118283. VBIMycSp106721_4071.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000384 Genomic DNA. Translation: ABG10078.1 .
RefSeqi YP_641134.1. NC_008146.1.

3D structure databases

ProteinModelPortali Q1B4V6.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 164756.Mmcs_3973.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABG10078 ; ABG10078 ; Mmcs_3973 .
GeneIDi 4112803.
KEGGi mmc:Mmcs_3973.
PATRICi 18118283. VBIMycSp106721_4071.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00223 ; UER00997 .
UPA00223 ; UER01001 .
BioCyci MSP164756:GHQ8-4015-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: MCS.

Entry informationi

Entry nameiKGD_MYCSS
AccessioniPrimary (citable) accession number: Q1B4V6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: July 11, 2006
Last modified: November 26, 2014
This is version 66 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