ODO1_ECOLI
ID ODO1_ECOLI Reviewed; 933 AA.
AC P0AFG3; P07015; P78225;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=2-oxoglutarate dehydrogenase E1 component;
DE EC=1.2.4.2 {ECO:0000269|PubMed:17367808};
DE AltName: Full=Alpha-ketoglutarate dehydrogenase;
GN Name=sucA; OrderedLocusNames=b0726, JW0715;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=6376123; DOI=10.1111/j.1432-1033.1984.tb08199.x;
RA Darlison M.G., Spencer M.E., Guest J.R.;
RT "Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate
RT dehydrogenase of Escherichia coli K12.";
RL Eur. J. Biochem. 141:351-359(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [6]
RP AMPYLATION AT THR-405, AND MUTAGENESIS OF SER-404 AND THR-405.
RX PubMed=30270044; DOI=10.1016/j.cell.2018.08.046;
RA Sreelatha A., Yee S.S., Lopez V.A., Park B.C., Kinch L.N., Pilch S.,
RA Servage K.A., Zhang J., Jiou J., Karasiewicz-Urbanska M., Lobocka M.,
RA Grishin N.V., Orth K., Kucharczyk R., Pawlowski K., Tomchick D.R.,
RA Tagliabracci V.S.;
RT "Protein AMPylation by an Evolutionarily Conserved Pseudokinase.";
RL Cell 175:809-821(2018).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, ACTIVITY REGULATION, SUBUNIT, INTERACTION WITH SUCB, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF HIS-260; HIS-298; HIS-313; ARG-337; TRP-533
RP AND ARG-710.
RX PubMed=17367808; DOI=10.1016/j.jmb.2007.01.080;
RA Frank R.A., Price A.J., Northrop F.D., Perham R.N., Luisi B.F.;
RT "Crystal structure of the E1 component of the Escherichia coli 2-
RT oxoglutarate dehydrogenase multienzyme complex.";
RL J. Mol. Biol. 368:639-651(2007).
CC -!- FUNCTION: E1 component of the 2-oxoglutarate dehydrogenase (OGDH)
CC complex which catalyzes the decarboxylation of 2-oxoglutarate, the
CC first step in the conversion of 2-oxoglutarate to succinyl-CoA and
CC CO(2). {ECO:0000269|PubMed:17367808}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-lipoyl-L-lysyl-[dihydrolipoyllysine-residue
CC succinyltransferase] + 2-oxoglutarate + H(+) = (R)-N(6)-(S(8)-
CC succinyldihydrolipoyl)-L-lysyl-[dihydrolipoyllysine-residue
CC succinyltransferase] + CO2; Xref=Rhea:RHEA:12188, Rhea:RHEA-
CC COMP:10483, Rhea:RHEA-COMP:10484, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:83099,
CC ChEBI:CHEBI:83120; EC=1.2.4.2;
CC Evidence={ECO:0000269|PubMed:17367808};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:12189;
CC Evidence={ECO:0000269|PubMed:17367808};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000305|PubMed:17367808};
CC -!- ACTIVITY REGULATION: Inhibited by oxaloacetate.
CC {ECO:0000269|PubMed:17367808}.
CC -!- SUBUNIT: Homodimer (PubMed:17367808). Part of the 2-oxoglutarate
CC dehydrogenase (OGDH) complex composed of E1 (2-oxoglutarate
CC dehydrogenase), E2 (dihydrolipoamide succinyltransferase) and E3
CC (dihydrolipoamide dehydrogenase); the complex contains multiple copies
CC of the three enzymatic components (E1, E2 and E3) (Probable). Interacts
CC (via N-terminus) with SucB, the E2 component of OGDH complex
CC (PubMed:17367808). {ECO:0000269|PubMed:17367808,
CC ECO:0000305|PubMed:17367808}.
CC -!- INTERACTION:
CC P0AFG3; P0AFG3: sucA; NbExp=2; IntAct=EBI-543523, EBI-543523;
CC P0AFG3; P0AFG6: sucB; NbExp=7; IntAct=EBI-543523, EBI-558621;
CC P0AFG3; P63389: yheS; NbExp=3; IntAct=EBI-543523, EBI-561198;
CC -!- DISRUPTION PHENOTYPE: Impaired growth in minimal medium containing
CC acetate as the sole carbon source. {ECO:0000269|PubMed:17367808}.
CC -!- MISCELLANEOUS: Binds AMP; however it is not clear if the binding is
CC physiologically relevant. {ECO:0000269|PubMed:17367808}.
CC -!- SIMILARITY: Belongs to the alpha-ketoglutarate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; J01619; AAA23897.1; -; Genomic_DNA.
DR EMBL; X00661; CAA25280.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73820.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35392.1; -; Genomic_DNA.
DR PIR; E64808; DEECOG.
DR RefSeq; NP_415254.1; NC_000913.3.
DR RefSeq; WP_001181473.1; NZ_STEB01000035.1.
DR PDB; 2JGD; X-ray; 2.60 A; A/B=1-933.
DR PDB; 6VEF; EM; 4.08 A; A/B=84-933.
DR PDBsum; 2JGD; -.
DR PDBsum; 6VEF; -.
DR AlphaFoldDB; P0AFG3; -.
DR SMR; P0AFG3; -.
DR BioGRID; 849680; 3.
DR ComplexPortal; CPX-3921; 2-oxoglutarate dehydrogenase complex.
DR DIP; DIP-36225N; -.
DR IntAct; P0AFG3; 13.
DR MINT; P0AFG3; -.
DR STRING; 511145.b0726; -.
DR SWISS-2DPAGE; P0AFG3; -.
DR jPOST; P0AFG3; -.
DR PaxDb; P0AFG3; -.
DR PRIDE; P0AFG3; -.
DR EnsemblBacteria; AAC73820; AAC73820; b0726.
DR EnsemblBacteria; BAA35392; BAA35392; BAA35392.
DR GeneID; 66671005; -.
DR GeneID; 945303; -.
DR KEGG; ecj:JW0715; -.
DR KEGG; eco:b0726; -.
DR PATRIC; fig|1411691.4.peg.1547; -.
DR EchoBASE; EB0972; -.
DR eggNOG; COG0567; Bacteria.
DR HOGENOM; CLU_004709_1_0_6; -.
DR InParanoid; P0AFG3; -.
DR OMA; RDSYCRT; -.
DR PhylomeDB; P0AFG3; -.
DR BioCyc; EcoCyc:E1O-MON; -.
DR BioCyc; MetaCyc:E1O-MON; -.
DR BRENDA; 1.2.1.105; 2026.
DR BRENDA; 1.2.4.2; 2026.
DR BRENDA; 2.2.1.5; 2026.
DR SABIO-RK; P0AFG3; -.
DR EvolutionaryTrace; P0AFG3; -.
DR PRO; PR:P0AFG3; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:ComplexPortal.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0045252; C:oxoglutarate dehydrogenase complex; IPI:ComplexPortal.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0004591; F:oxoglutarate dehydrogenase (succinyl-transferring) activity; IDA:EcoCyc.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IDA:EcoCyc.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IDA:ComplexPortal.
DR Gene3D; 3.40.50.11610; -; 1.
DR InterPro; IPR032106; 2-oxogl_dehyd_N.
DR InterPro; IPR011603; 2oxoglutarate_DH_E1.
DR InterPro; IPR001017; DH_E1.
DR InterPro; IPR031717; KGD_C.
DR InterPro; IPR042179; KGD_C_sf.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR005475; Transketolase-like_Pyr-bd.
DR PANTHER; PTHR23152; PTHR23152; 1.
DR Pfam; PF16078; 2-oxogl_dehyd_N; 1.
DR Pfam; PF00676; E1_dh; 1.
DR Pfam; PF16870; OxoGdeHyase_C; 1.
DR Pfam; PF02779; Transket_pyr; 1.
DR PIRSF; PIRSF000157; Oxoglu_dh_E1; 1.
DR SMART; SM00861; Transket_pyr; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR TIGRFAMs; TIGR00239; 2oxo_dh_E1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleotide-binding; Oxidoreductase; Phosphoprotein;
KW Reference proteome; Thiamine pyrophosphate; Tricarboxylic acid cycle.
FT CHAIN 1..933
FT /note="2-oxoglutarate dehydrogenase E1 component"
FT /id="PRO_0000162191"
FT MOD_RES 405
FT /note="O-AMP-threonine; by ydiU"
FT /evidence="ECO:0000269|PubMed:30270044"
FT MUTAGEN 260
FT /note="H->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 298
FT /note="H->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 313
FT /note="H->A: Mild reduction in growth in presence of
FT acetate or glucose as sole source of carbon; when
FT associated with A-337."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 313
FT /note="H->Q: No growth defect in presence of acetate or
FT glucose as sole source of carbon."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 337
FT /note="R->A: Mild reduction in growth in presence of
FT acetate or glucose as sole source of carbon; when
FT associated with A-313."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 404
FT /note="S->A: No loss of AMPylation by YdiU."
FT /evidence="ECO:0000269|PubMed:30270044"
FT MUTAGEN 405
FT /note="T->A: Severe reduction in AMPylation by YdiU."
FT /evidence="ECO:0000269|PubMed:30270044"
FT MUTAGEN 533
FT /note="W->A: Mild reduction in growth in presence of
FT acetate or glucose as sole source of carbon; when
FT associated with A-710."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 533
FT /note="W->I: No growth defect in presence of acetate or
FT glucose as sole source of carbon."
FT /evidence="ECO:0000269|PubMed:17367808"
FT MUTAGEN 710
FT /note="R->A: Mild reduction in growth in presence of
FT acetate or glucose as sole source of carbon; when
FT associated with A-533."
FT /evidence="ECO:0000269|PubMed:17367808"
FT CONFLICT 454
FT /note="C -> S (in Ref. 1; AAA23897/CAA25280)"
FT /evidence="ECO:0000305"
FT HELIX 85..102
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 103..106
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 126..129
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 132..136
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 153..165
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 166..171
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 178..188
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 197..220
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 235..247
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 248..250
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 263..269
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 275..282
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 301..307
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 310..316
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 321..324
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 326..338
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 346..348
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 349..356
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 357..362
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 365..372
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 376..378
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 384..389
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 408..413
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 414..416
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 419..423
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 427..444
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 448..453
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 474..478
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 483..492
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 493..495
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 499..515
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 528..530
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 534..536
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 551..560
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 572..585
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 593..605
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 606..608
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 611..615
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 616..620
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 629..631
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 633..636
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 641..643
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 652..655
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 661..674
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 678..683
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 687..693
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 694..699
FT /evidence="ECO:0007829|PDB:2JGD"
FT TURN 700..703
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 704..708
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 715..719
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 723..725
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 734..739
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 747..749
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 754..766
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 773..777
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 780..783
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 791..796
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 801..803
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 811..813
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 816..820
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 824..834
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 839..845
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 847..850
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 853..860
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 861..863
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 868..876
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 879..881
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 882..890
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 898..904
FT /evidence="ECO:0007829|PDB:2JGD"
FT STRAND 908..911
FT /evidence="ECO:0007829|PDB:2JGD"
FT HELIX 915..930
FT /evidence="ECO:0007829|PDB:2JGD"
SQ SEQUENCE 933 AA; 105062 MW; EAEF8429EC31E749 CRC64;
MQNSALKAWL DSSYLSGANQ SWIEQLYEDF LTDPDSVDAN WRSTFQQLPG TGVKPDQFHS
QTREYFRRLA KDASRYSSTI SDPDTNVKQV KVLQLINAYR FRGHQHANLD PLGLWQQDKV
ADLDPSFHDL TEADFQETFN VGSFASGKET MKLGELLEAL KQTYCGPIGA EYMHITSTEE
KRWIQQRIES GRATFNSEEK KRFLSELTAA EGLERYLGAK FPGAKRFSLE GGDALIPMLK
EMIRHAGNSG TREVVLGMAH RGRLNVLVNV LGKKPQDLFD EFAGKHKEHL GTGDVKYHMG
FSSDFQTDGG LVHLALAFNP SHLEIVSPVV IGSVRARLDR LDEPSSNKVL PITIHGDAAV
TGQGVVQETL NMSKARGYEV GGTVRIVINN QVGFTTSNPL DARSTPYCTD IGKMVQAPIF
HVNADDPEAV AFVTRLALDF RNTFKRDVFI DLVCYRRHGH NEADEPSATQ PLMYQKIKKH
PTPRKIYADK LEQEKVATLE DATEMVNLYR DALDAGDCVV AEWRPMNMHS FTWSPYLNHE
WDEEYPNKVE MKRLQELAKR ISTVPEAVEM QSRVAKIYGD RQAMAAGEKL FDWGGAENLA
YATLVDEGIP VRLSGEDSGR GTFFHRHAVI HNQSNGSTYT PLQHIHNGQG AFRVWDSVLS
EEAVLAFEYG YATAEPRTLT IWEAQFGDFA NGAQVVIDQF ISSGEQKWGR MCGLVMLLPH
GYEGQGPEHS SARLERYLQL CAEQNMQVCV PSTPAQVYHM LRRQALRGMR RPLVVMSPKS
LLRHPLAVSS LEELANGTFL PAIGEIDELD PKGVKRVVMC SGKVYYDLLE QRRKNNQHDV
AIVRIEQLYP FPHKAMQEVL QQFAHVKDFV WCQEEPLNQG AWYCSQHHFR EVIPFGASLR
YAGRPASASP AVGYMSVHQK QQQDLVNDAL NVE
