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A5U1U6

- KGD_MYCTA

UniProt

A5U1U6 - KGD_MYCTA

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Protein
Multifunctional 2-oxoglutarate metabolism enzyme
Gene
kgd, MRA_1256
Organism
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
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.

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 sitei316 – 3161Proton acceptor; for succinyltransferase activity By similarity
Binding sitei581 – 58112-oxoglutarate By similarity
Binding sitei606 – 60612-oxoglutarate By similarity
Metal bindingi649 – 6491Magnesium By similarity
Metal bindingi682 – 6821Magnesium By similarity
Metal bindingi684 – 6841Magnesium; via carbonyl oxygen By similarity
Binding sitei956 – 9561Thiamine pyrophosphate By similarity
Binding sitei1024 – 102412-oxoglutarate By similarity
Binding sitei1042 – 10421Allosteric activator By similarity
Binding sitei1058 – 10581Allosteric activator By similarity
Binding sitei1146 – 11461Allosteric activator By 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
Complete GO annotation...

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

BioCyciMTUB419947:GJ8N-1295-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:MRA_1256
OrganismiMycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
Taxonomic identifieri419947 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
ProteomesiUP000001988: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12311231Multifunctional 2-oxoglutarate metabolism enzyme
PRO_0000310723Add
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.

Protein-protein interaction databases

STRINGi419947.MRA_1256.

Structurei

3D structure databases

ProteinModelPortaliA5U1U6.
SMRiA5U1U6. Positions 116-335, 367-1231.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 41412-oxoglutarate dehydrogenase E1, N-terminal part
Add
BLAST
Regioni42 – 8847Linker
Add
BLAST
Regioni89 – 337249Succinyltransferase E2
Add
BLAST
Regioni338 – 12318942-oxoglutarate dehydrogenase E1, C-terminal part
Add
BLAST
Regioni541 – 5422Thiamine pyrophosphate binding By similarity
Regioni606 – 6083Thiamine pyrophosphate binding By similarity
Regioni649 – 6513Thiamine pyrophosphate binding By similarity
Regioni1093 – 10964Allosteric activator By similarity
Regioni1153 – 11542Allosteric activator By similarity

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili787 – 81731 Reviewed prediction
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi61 – 11353Ala-rich
Add
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.

A5U1U6-1 [UniParc]FASTAAdd to Basket

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MANISSPFGQ NEWLVEEMYR KFRDDPSSVD PSWHEFLVDY SPEPTSQPAA     50
EPTRVTSPLV AERAAAAAPQ APPKPADTAA AGNGVVAALA AKTAVPPPAE 100
GDEVAVLRGA AAAVVKNMSA SLEVPTATSV RAVPAKLLID NRIVINNQLK 150
RTRGGKISFT HLLGYALVQA VKKFPNMNRH YTEVDGKPTA VTPAHTNLGL 200
AIDLQGKDGK RSLVVAGIKR CETMRFAQFV TAYEDIVRRA RDGKLTTEDF 250
AGVTISLTNP GTIGTVHSVP RLMPGQGAII GVGAMEYPAE FQGASEERIA 300
ELGIGKLITL TSTYDHRIIQ GAESGDFLRT IHELLLSDGF WDEVFRELSI 350
PYLPVRWSTD NPDSIVDKNA RVMNLIAAYR NRGHLMADTD PLRLDKARFR 400
SHPDLEVLTH GLTLWDLDRV FKVDGFAGAQ YKKLRDVLGL LRDAYCRHIG 450
VEYAHILDPE QKEWLEQRVE TKHVKPTVAQ QKYILSKLNA AEAFETFLQT 500
KYVGQKRFSL EGAESVIPMM DAAIDQCAEH GLDEVVIGMP HRGRLNVLAN 550
IVGKPYSQIF TEFEGNLNPS QAHGSGDVKY HLGATGLYLQ MFGDNDIQVS 600
LTANPSHLEA VDPVLEGLVR AKQDLLDHGS IDSDGQRAFS VVPLMLHGDA 650
AFAGQGVVAE TLNLANLPGY RVGGTIHIIV NNQIGFTTAP EYSRSSEYCT 700
DVAKMIGAPI FHVNGDDPEA CVWVARLAVD FRQRFKKDVV IDMLCYRRRG 750
HNEGDDPSMT NPYVYDVVDT KRGARKSYTE ALIGRGDISM KEAEDALRDY 800
QGQLERVFNE VRELEKHGVQ PSESVESDQM IPAGLATAVD KSLLARIGDA 850
FLALPNGFTA HPRVQPVLEK RREMAYEGKI DWAFGELLAL GSLVAEGKLV 900
RLSGQDSRRG TFSQRHSVLI DRHTGEEFTP LQLLATNSDG SPTGGKFLVY 950
DSPLSEYAAV GFEYGYTVGN PDAVVLWEAQ FGDFVNGAQS IIDEFISSGE 1000
AKWGQLSNVV LLLPHGHEGQ GPDHTSARIE RFLQLWAEGS MTIAMPSTPS 1050
NYFHLLRRHA LDGIQRPLIV FTPKSMLRHK AAVSEIKDFT EIKFRSVLEE 1100
PTYEDGIGDR NKVSRILLTS GKLYYELAAR KAKDNRNDLA IVRLEQLAPL 1150
PRRRLRETLD RYENVKEFFW VQEEPANQGA WPRFGLELPE LLPDKLAGIK 1200
RISRRAMSAP SSGSSKVHAV EQQEILDEAF G 1231
Length:1,231
Mass (Da):135,902
Last modified:November 13, 2007 - v2
Checksum:i96C255612BA12889
GO

Sequence cautioni

The sequence ABQ72996.1 differs from that shown. Reason: Erroneous initiation.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000611 Genomic DNA. Translation: ABQ72996.1. Different initiation.
RefSeqiYP_001282558.1. NC_009525.1.

Genome annotation databases

EnsemblBacteriaiABQ72996; ABQ72996; MRA_1256.
GeneIDi5214632.
KEGGimra:MRA_1256.
PATRICi18142389. VBIMycTub106795_1401.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000611 Genomic DNA. Translation: ABQ72996.1 . Different initiation.
RefSeqi YP_001282558.1. NC_009525.1.

3D structure databases

ProteinModelPortali A5U1U6.
SMRi A5U1U6. Positions 116-335, 367-1231.
ModBasei Search...

Protein-protein interaction databases

STRINGi 419947.MRA_1256.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABQ72996 ; ABQ72996 ; MRA_1256 .
GeneIDi 5214632.
KEGGi mra:MRA_1256.
PATRICi 18142389. VBIMycTub106795_1401.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00223 ; UER00997 .
UPA00223 ; UER01001 .
BioCyci MTUB419947:GJ8N-1295-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. "Complete genomic sequence of Mycobacterium tuberculosis strain H37Ra, a non-pathogenic variant closely related to the well-characterized pathogenic strain H37Rv."
    Wang S.Y., Zheng H.J., Lv L.D., Wang B.F., Zhang X.L., Pu S.Y., Zhu G.F., Wang H.H., Zhao G.P., Zhang Y.
    Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25177 / H37Ra.

Entry informationi

Entry nameiKGD_MYCTA
AccessioniPrimary (citable) accession number: A5U1U6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: November 13, 2007
Last modified: June 11, 2014
This is version 52 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

Documents

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

External Data

Dasty 3

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