O50463 (KGD_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Multifunctional 2-oxoglutarate metabolism enzyme

Alternative name(s):
2-hydroxy-3-oxoadipate synthase
Short name=HOA synthase
Short name=HOAS
EC=2.2.1.5
2-oxoglutarate carboxy-lyase
2-oxoglutarate decarboxylase
Alpha-ketoglutarate decarboxylase
Short name=KG decarboxylase
Short name=KGD
EC=4.1.1.71
Alpha-ketoglutarate-glyoxylate carboligase

Including the following 2 domains:

1. 2-oxoglutarate dehydrogenase E1 component
   Short name=ODH E1 component
   EC=1.2.4.2
   Alternative name(s):
   Alpha-ketoglutarate dehydrogenase E1 component
   Short name=KDH E1 component
2. 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 names

Name:	kgd
Ordered Locus Names:	Rv1248c, MT1286

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	1231 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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, which can endow M.tuberculosis with the metabolic plasticity required for growth on diverse host-derived carbon sources. Appears to play a predominant role in growth on carbohydrates as the sole carbon source, and only a minimal role during growth on fatty acids. Ref.3 Ref.4 Ref.6 Ref.8 Ref.9
Catalytic activity	2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO2. Ref.8 Ref.9 2-oxoglutarate = succinate semialdehyde + CO2. Ref.8 Ref.9 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2. Ref.8 Ref.9 Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine. Ref.8 Ref.9
Cofactor	Magnesium. Ref.4 Ref.8 Thiamine pyrophosphate. Ref.4 Ref.8
Enzyme regulation	Alpha-ketoglutarate dehydrogenase and decarboxylase activities are inhibited by unphosphorylated GarA, and allosterically activated by acetyl-CoA, the main substrate of the TCA cycle. Ref.7 Ref.9
Pathway	Carbohydrate metabolism; tricarboxylic acid cycle; succinate from 2-oxoglutarate (transferase route): step 1/2. Carbohydrate metabolism; tricarboxylic acid cycle; succinyl-CoA from 2-oxoglutarate (dehydrogenase route): step 1/1.
Subunit structure	Homodimer By similarity. 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. Interacts with the FHA domain of unphosphorylated GarA. Ref.5 Ref.7
Domain	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.
Disruption phenotype	Attempts to disrupt Rv1248c in M.tuberculosis H37Rv and Erdman strains by homologous recombination were unsuccessful, raising the possibility that Rv1248c may be essential (Ref.8). However, deletion mutants were readily obtained in a strain derived from H37Rv in Ref.6. The mutant strain grows as well as wild-type in medium containing both carbohydrates (dextrose and glycerol) and fatty acids, under a CO2 enriched atmosphere, but shows a marked growth defect when grown in medium containing carbohydrates as the sole carbon source in the presence of CO2. Simultaneous disruption of korAB and kgd results in strict dependence upon the glyoxylate shunt for growth. Growth of the kgd mutant strain on fatty acids as the sole carbon source is similar to that of the wild type strain regardless of the presence of CO2. But cells lacking both korAB and kgd is significantly more retarded for growth on fatty acids than is either korAB or kgd deleted mutant alone. Ref.6 Ref.8
Sequence similarities	Belongs to the 2-oxoacid dehydrogenase family. Kgd subfamily.
Caution	Was originally (Ref.1 and Ref.2) annotated as sucA because of sequence similarity, but this protein was shown (Ref.3) not to be able to serve as the E1 component of 2-oxoglutarate dehydrogenase (ODH). However, it was later shown that this protein does in fact sustain ODH activity (Ref.9), and requires specific activation by acetyl-CoA.
Biophysicochemical properties	Kinetic parameters: KM=0.48 mM for 2-oxoglutarate Ref.4 KM=0.196 mM for magnesium ions KM=0.019 mM for thiamine pyrophosphate
Sequence caution	The sequence CAA15904.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Domain	Coiled coil
Ligand	Magnesium Metal-binding Thiamine pyrophosphate
Molecular function	Acyltransferase Decarboxylase Lyase Oxidoreductase Transferase
Technical term	Allosteric enzyme Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	2-oxoglutarate metabolic process Inferred from direct assay Ref.8. Source: MTBBASE growth Inferred from mutant phenotype PubMed 12657046. Source: MTBBASE tricarboxylic acid cycle Inferred from direct assay Ref.4. Source: MTBBASE
Cellular_component	cell wall Inferred from direct assay PubMed 20825248. Source: MTBBASE plasma membrane Inferred from direct assay PubMed 15525680. Source: MTBBASE pyruvate dehydrogenase complex Inferred from direct assay Ref.3. Source: MTBBASE
Molecular_function	2-hydroxy-3-oxoadipate synthase activity Inferred from direct assay Ref.8. Source: MTBBASE 2-oxoglutarate decarboxylase activity Inferred from direct assay Ref.4. Source: MTBBASE dihydrolipoyllysine-residue succinyltransferase activity Inferred from electronic annotation. Source: EC electron carrier activity Inferred from direct assay Ref.3. Source: MTBBASE magnesium ion binding Inferred from direct assay Ref.4Ref.8. Source: MTBBASE oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor Inferred from electronic annotation. Source: InterPro thiamine pyrophosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
garA	P64897	2	EBI-6405560,EBI-6405522

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1231	1231	Multifunctional 2-oxoglutarate metabolism enzyme		PRO_0000310722
Regions
	Region	1 – 41	41	2-oxoglutarate dehydrogenase E1, N-terminal part
	Region	42 – 88	47	Linker
	Region	89 – 337	249	Succinyltransferase E2
	Region	338 – 1231	894	2-oxoglutarate dehydrogenase E1, C-terminal part
	Region	541 – 542	2	Thiamine pyrophosphate binding By similarity
	Region	606 – 608	3	Thiamine pyrophosphate binding By similarity
	Region	649 – 651	3	Thiamine pyrophosphate binding By similarity
	Region	1093 – 1096	4	Allosteric activator By similarity
	Region	1153 – 1154	2	Allosteric activator By similarity
	Coiled coil	787 – 817	31	Potential
	Compositional bias	61 – 113	53	Ala-rich
Sites
	Active site	316	1	Proton acceptor; for succinyltransferase activity By similarity
	Metal binding	649	1	Magnesium By similarity
	Metal binding	682	1	Magnesium By similarity
	Metal binding	684	1	Magnesium; via carbonyl oxygen By similarity
	Binding site	581	1	2-oxoglutarate By similarity
	Binding site	606	1	2-oxoglutarate By similarity
	Binding site	956	1	Thiamine pyrophosphate By similarity
	Binding site	1024	1	2-oxoglutarate By similarity
	Binding site	1042	1	Allosteric activator By similarity
	Binding site	1058	1	Allosteric activator By similarity
	Binding site	1146	1	Allosteric activator By similarity

Sequences

	Sequence		Length	Mass (Da)
	O50463 [UniParc]. Last modified November 13, 2007. Version 4. Checksum: 96C255612BA12889	FASTA	1,231	135,902
	10 20 30 40 50 60 MANISSPFGQ NEWLVEEMYR KFRDDPSSVD PSWHEFLVDY SPEPTSQPAA EPTRVTSPLV 70 80 90 100 110 120 AERAAAAAPQ APPKPADTAA AGNGVVAALA AKTAVPPPAE GDEVAVLRGA AAAVVKNMSA 130 140 150 160 170 180 SLEVPTATSV RAVPAKLLID NRIVINNQLK RTRGGKISFT HLLGYALVQA VKKFPNMNRH 190 200 210 220 230 240 YTEVDGKPTA VTPAHTNLGL AIDLQGKDGK RSLVVAGIKR CETMRFAQFV TAYEDIVRRA 250 260 270 280 290 300 RDGKLTTEDF AGVTISLTNP GTIGTVHSVP RLMPGQGAII GVGAMEYPAE FQGASEERIA 310 320 330 340 350 360 ELGIGKLITL TSTYDHRIIQ GAESGDFLRT IHELLLSDGF WDEVFRELSI PYLPVRWSTD 370 380 390 400 410 420 NPDSIVDKNA RVMNLIAAYR NRGHLMADTD PLRLDKARFR SHPDLEVLTH GLTLWDLDRV 430 440 450 460 470 480 FKVDGFAGAQ YKKLRDVLGL LRDAYCRHIG VEYAHILDPE QKEWLEQRVE TKHVKPTVAQ 490 500 510 520 530 540 QKYILSKLNA AEAFETFLQT KYVGQKRFSL EGAESVIPMM DAAIDQCAEH GLDEVVIGMP 550 560 570 580 590 600 HRGRLNVLAN IVGKPYSQIF TEFEGNLNPS QAHGSGDVKY HLGATGLYLQ MFGDNDIQVS 610 620 630 640 650 660 LTANPSHLEA VDPVLEGLVR AKQDLLDHGS IDSDGQRAFS VVPLMLHGDA AFAGQGVVAE 670 680 690 700 710 720 TLNLANLPGY RVGGTIHIIV NNQIGFTTAP EYSRSSEYCT DVAKMIGAPI FHVNGDDPEA 730 740 750 760 770 780 CVWVARLAVD FRQRFKKDVV IDMLCYRRRG HNEGDDPSMT NPYVYDVVDT KRGARKSYTE 790 800 810 820 830 840 ALIGRGDISM KEAEDALRDY QGQLERVFNE VRELEKHGVQ PSESVESDQM IPAGLATAVD 850 860 870 880 890 900 KSLLARIGDA FLALPNGFTA HPRVQPVLEK RREMAYEGKI DWAFGELLAL GSLVAEGKLV 910 920 930 940 950 960 RLSGQDSRRG TFSQRHSVLI DRHTGEEFTP LQLLATNSDG SPTGGKFLVY DSPLSEYAAV 970 980 990 1000 1010 1020 GFEYGYTVGN PDAVVLWEAQ FGDFVNGAQS IIDEFISSGE AKWGQLSNVV LLLPHGHEGQ 1030 1040 1050 1060 1070 1080 GPDHTSARIE RFLQLWAEGS MTIAMPSTPS NYFHLLRRHA LDGIQRPLIV FTPKSMLRHK 1090 1100 1110 1120 1130 1140 AAVSEIKDFT EIKFRSVLEE PTYEDGIGDR NKVSRILLTS GKLYYELAAR KAKDNRNDLA 1150 1160 1170 1180 1190 1200 IVRLEQLAPL PRRRLRETLD RYENVKEFFW VQEEPANQGA WPRFGLELPE LLPDKLAGIK 1210 1220 1230 RISRRAMSAP SSGSSKVHAV EQQEILDEAF G

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"Mycobacterium tuberculosis appears to lack alpha-ketoglutarate dehydrogenase and encodes pyruvate dehydrogenase in widely separated genes." Tian J., Bryk R., Shi S., Erdjument-Bromage H., Tempst P., Nathan C. Mol. Microbiol. 57:859-868(2005) [PubMed] [Europe PMC] [Abstract] Cited for: LACK OF FUNCTION AS A 2-OXOGLUTARATE DEHYDROGENASE COMPONENT. Strain: ATCC 25618 / H37Rv.
[4]	"Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: identification of alpha-ketoglutarate decarboxylase." Tian J., Bryk R., Itoh M., Suematsu M., Nathan C. Proc. Natl. Acad. Sci. U.S.A. 102:10670-10675(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A 2-OXOGLUTARATE DECARBOXYLASE, COFACTORS, ROLE IN A VARIANT TCA CYCLE, KINETIC PARAMETERS. Strain: ATCC 25618 / H37Rv.
[5]	"Regulation of glutamate metabolism by protein kinases in mycobacteria." O'Hare H.M., Duran R., Cervenansky C., Bellinzoni M., Wehenkel A.M., Pritsch O., Obal G., Baumgartner J., Vialaret J., Johnsson K., Alzari P.M. Mol. Microbiol. 70:1408-1423(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH GARA. Strain: ATCC 25618 / H37Rv.
[6]	"An anaerobic-type alpha-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis." Baughn A.D., Garforth S.J., Vilcheze C., Jacobs W.R. Jr. PLoS Pathog. 5:E1000662-E1000662(2009) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE, ROLE IN TCA CYCLE. Strain: ATCC 25618 / H37Rv.
[7]	"An intramolecular switch regulates phosphoindependent FHA domain interactions in Mycobacterium tuberculosis." Nott T.J., Kelly G., Stach L., Li J., Westcott S., Patel D., Hunt D.M., Howell S., Buxton R.S., O'Hare H.M., Smerdon S.J. Sci. Signal. 2:RA12-RA12(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION, INTERACTION WITH GARA. Strain: ATCC 25618 / H37Rv.
[8]	"Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase." de Carvalho L.P., Zhao H., Dickinson C.E., Arango N.M., Lima C.D., Fischer S.M., Ouerfelli O., Nathan C., Rhee K.Y. Chem. Biol. 17:323-332(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A HOA SYNTHASE, CATALYTIC ACTIVITY, COFACTORS, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[9]	"Functional plasticity and allosteric regulation of alpha-ketoglutarate decarboxylase in central mycobacterial metabolism." Wagner T., Bellinzoni M., Wehenkel A., O'Hare H.M., Alzari P.M. Chem. Biol. 18:1011-1020(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A MULTIFUNCTIONAL ENZYME, CATALYTIC ACTIVITY, ENZYME REGULATION. Strain: ATCC 25618 / H37Rv.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BX842576 Genomic DNA. Translation: CAA15904.1. Different initiation. AE000516 Genomic DNA. Translation: AAK45544.1. AL123456 Genomic DNA. Translation: CCP44004.1.
PIR	G70953.
RefSeq	NP_335730.1. NC_002755.2.
3D structure databases
ProteinModelPortal	O50463.
SMR	O50463. Positions 116-335, 367-1231.
ModBase	Search...
Protein-protein interaction databases
IntAct	O50463. 1 interaction.
STRING	83332.Rv1248c.
Proteomic databases
PRIDE	O50463.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAK45544; AAK45544; MT1286.
GeneID	924785.
KEGG	mtc:MT1286. mtu:Rv1248c.
PATRIC	18124592. VBIMycTub22151_1415.
Organism-specific databases
TubercuList	Rv1248c.
Phylogenomic databases
eggNOG	COG0508.
HOGENOM	HOG000259587.
KO	K01616.
OMA	IIKRGGA.
ProtClustDB	PRK12270.
Enzyme and pathway databases
UniPathway	UPA00223; UER00997. UPA00223; UER01001.
Family and domain databases
Gene3D	3.30.559.10. 1 hit.
InterPro	IPR001078. 2-oxoacid_DH_actylTfrase. IPR011603. 2oxoglutarate_DH_E1. IPR023213. CAT-like_dom. IPR001017. DH_E1. IPR005475. Transketolase-like_Pyr-bd. [Graphical view]
PANTHER	PTHR23152. PTHR23152. 1 hit.
Pfam	PF00198. 2-oxoacid_dh. 1 hit. PF00676. E1_dh. 1 hit. PF02779. Transket_pyr. 1 hit. [Graphical view]
PIRSF	PIRSF000157. Oxoglu_dh_E1. 1 hit.
SMART	SM00861. Transket_pyr. 1 hit. [Graphical view]
TIGRFAMs	TIGR00239. 2oxo_dh_E1. 1 hit.
ProtoNet	Search...

Entry information

Entry name

KGD_MYCTU

Accession

Primary (citable) accession number: O50463
Secondary accession number(s): L0T8T9, Q7D8I9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 13, 2007
Last sequence update:	November 13, 2007
Last modified:	May 1, 2013
This is version 89 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program