ODO2_ECOLI
ID ODO2_ECOLI Reviewed; 405 AA.
AC P0AFG6; P07016;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex;
DE EC=2.3.1.61 {ECO:0000305|PubMed:17367808};
DE AltName: Full=2-oxoglutarate dehydrogenase complex component E2;
DE Short=OGDC-E2;
DE AltName: Full=Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex;
GN Name=sucB; OrderedLocusNames=b0727, JW0716;
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=6376124; DOI=10.1111/j.1432-1033.1984.tb08200.x;
RA Spencer M.E., Darlison M.G., Stephens P.E., Duckenfield I.K., Guest J.R.;
RT "Nucleotide sequence of the sucB gene encoding the dihydrolipoamide
RT succinyltransferase of Escherichia coli K12 and homology with the
RT corresponding acetyltransferase.";
RL Eur. J. Biochem. 141:361-374(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 PROTEIN SEQUENCE OF 4-10.
RC STRAIN=K12;
RX PubMed=17895580; DOI=10.1266/ggs.82.291;
RA Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
RT "A role of RnlA in the RNase LS activity from Escherichia coli.";
RL Genes Genet. Syst. 82:291-299(2007).
RN [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-12.
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 [7]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [8]
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 [9]
RP FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH SUCA.
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).
RN [10]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-148, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
RN [11]
RP STRUCTURE BY NMR OF 1-81, AND LIPOYLATION AT LYS-44.
RX PubMed=8950276; DOI=10.1006/jmbi.1996.0632;
RA Ricaud P.M., Howard M.J., Roberts E.L., Broadhurst R.W., Perham R.N.;
RT "Three-dimensional structure of the lipoyl domain from the dihydrolipoyl
RT succinyltransferase component of the 2-oxoglutarate dehydrogenase
RT multienzyme complex of Escherichia coli.";
RL J. Mol. Biol. 264:179-190(1996).
RN [12]
RP STRUCTURE BY NMR OF 104-153.
RX PubMed=1554728; DOI=10.1021/bi00128a021;
RA Robien M.A., Clore G.M., Omichinski J.G., Perham R.N., Appella E.,
RA Sakaguchi K., Gronenborn A.M.;
RT "Three-dimensional solution structure of the E3-binding domain of the
RT dihydrolipoamide succinyltransferase core from the 2-oxoglutarate
RT dehydrogenase multienzyme complex of Escherichia coli.";
RL Biochemistry 31:3463-3471(1992).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405, SUBUNIT, AND ACTIVE SITE.
RX PubMed=9677295; DOI=10.1006/jmbi.1998.1924;
RA Knapp J.E., Mitchell D.T., Yazdi M.A., Ernst S.R., Reed L.J., Hackert M.L.;
RT "Crystal structure of the truncated cubic core component of the Escherichia
RT coli 2-oxoglutarate dehydrogenase multienzyme complex.";
RL J. Mol. Biol. 280:655-668(1998).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405, SUBUNIT, AND ACTIVE SITE.
RX PubMed=10739245; DOI=10.1110/ps.9.1.37;
RA Knapp J.E., Carroll D., Lawson J.E., Ernst S.R., Reed L.J., Hackert M.L.;
RT "Expression, purification, and structural analysis of the trimeric form of
RT the catalytic domain of the Escherichia coli dihydrolipoamide
RT succinyltransferase.";
RL Protein Sci. 9:37-48(2000).
CC -!- FUNCTION: E2 component of the 2-oxoglutarate dehydrogenase (OGDH)
CC complex which catalyzes the second step in the conversion of 2-
CC oxoglutarate to succinyl-CoA and CO(2). {ECO:0000305|PubMed:17367808}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-dihydrolipoyl-L-lysyl-[2-oxoglutarate dehydrogenase
CC complex component E2] + succinyl-CoA = (R)-N(6)-(S(8)-
CC succinyldihydrolipoyl)-L-lysyl-[2-oxoglutarate dehydrogenase complex
CC component E2] + CoA; Xref=Rhea:RHEA:15213, Rhea:RHEA-COMP:10581,
CC Rhea:RHEA-COMP:10582, ChEBI:CHEBI:57287, ChEBI:CHEBI:57292,
CC ChEBI:CHEBI:83100, ChEBI:CHEBI:83120; EC=2.3.1.61;
CC Evidence={ECO:0000305|PubMed:17367808};
CC -!- COFACTOR:
CC Name=(R)-lipoate; Xref=ChEBI:CHEBI:83088;
CC Note=Binds 1 lipoyl cofactor covalently.;
CC -!- PATHWAY: Amino-acid degradation; L-lysine degradation via saccharopine
CC pathway; glutaryl-CoA from L-lysine: step 6/6.
CC -!- SUBUNIT: Forms a 24-polypeptide structural core with octahedral
CC symmetry (PubMed:9677295, PubMed:10739245). 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 with SucA (via N-terminus), the E1 component of OGDH complex
CC (PubMed:17367808). {ECO:0000269|PubMed:10739245,
CC ECO:0000269|PubMed:17367808, ECO:0000269|PubMed:9677295,
CC ECO:0000305|PubMed:17367808}.
CC -!- INTERACTION:
CC P0AFG6; P0A9P0: lpdA; NbExp=3; IntAct=EBI-558621, EBI-542856;
CC P0AFG6; P0AFG3: sucA; NbExp=7; IntAct=EBI-558621, EBI-543523;
CC P0AFG6; P77717: ybaY; NbExp=3; IntAct=EBI-558621, EBI-558645;
CC -!- SIMILARITY: Belongs to the 2-oxoacid dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; J01619; AAA23898.1; -; Genomic_DNA.
DR EMBL; X00664; CAA25284.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73821.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35393.1; -; Genomic_DNA.
DR EMBL; X00661; CAA25281.1; -; Genomic_DNA.
DR PIR; F64808; XUECSD.
DR RefSeq; NP_415255.1; NC_000913.3.
DR RefSeq; WP_000099823.1; NZ_SSZK01000033.1.
DR PDB; 1BAL; NMR; -; A=104-153.
DR PDB; 1BBL; NMR; -; A=104-153.
DR PDB; 1C4T; X-ray; 3.00 A; A/B/C=173-405.
DR PDB; 1E2O; X-ray; 3.00 A; A=173-405.
DR PDB; 1PMR; NMR; -; A=2-81.
DR PDB; 1SCZ; X-ray; 2.20 A; A=173-405.
DR PDB; 1W4H; NMR; -; A=109-153.
DR PDB; 2BTG; NMR; -; A=109-153.
DR PDB; 2BTH; NMR; -; A=109-153.
DR PDB; 2WXC; NMR; -; A=109-153.
DR PDB; 6PBR; X-ray; 3.00 A; A/B/C/D/E/F=173-405.
DR PDBsum; 1BAL; -.
DR PDBsum; 1BBL; -.
DR PDBsum; 1C4T; -.
DR PDBsum; 1E2O; -.
DR PDBsum; 1PMR; -.
DR PDBsum; 1SCZ; -.
DR PDBsum; 1W4H; -.
DR PDBsum; 2BTG; -.
DR PDBsum; 2BTH; -.
DR PDBsum; 2WXC; -.
DR PDBsum; 6PBR; -.
DR AlphaFoldDB; P0AFG6; -.
DR BMRB; P0AFG6; -.
DR SASBDB; P0AFG6; -.
DR SMR; P0AFG6; -.
DR BioGRID; 4259945; 23.
DR BioGRID; 849684; 3.
DR ComplexPortal; CPX-3921; 2-oxoglutarate dehydrogenase complex.
DR DIP; DIP-35787N; -.
DR IntAct; P0AFG6; 39.
DR STRING; 511145.b0727; -.
DR iPTMnet; P0AFG6; -.
DR SWISS-2DPAGE; P0AFG6; -.
DR jPOST; P0AFG6; -.
DR PaxDb; P0AFG6; -.
DR PRIDE; P0AFG6; -.
DR EnsemblBacteria; AAC73821; AAC73821; b0727.
DR EnsemblBacteria; BAA35393; BAA35393; BAA35393.
DR GeneID; 58460903; -.
DR GeneID; 945307; -.
DR KEGG; ecj:JW0716; -.
DR KEGG; eco:b0727; -.
DR PATRIC; fig|1411691.4.peg.1546; -.
DR EchoBASE; EB0973; -.
DR eggNOG; COG0508; Bacteria.
DR HOGENOM; CLU_016733_0_0_6; -.
DR InParanoid; P0AFG6; -.
DR OMA; MKVPSPG; -.
DR PhylomeDB; P0AFG6; -.
DR BioCyc; EcoCyc:E2O-MON; -.
DR BioCyc; MetaCyc:E2O-MON; -.
DR BRENDA; 1.2.1.105; 2026.
DR BRENDA; 2.3.1.61; 2026.
DR SABIO-RK; P0AFG6; -.
DR UniPathway; UPA00868; UER00840.
DR EvolutionaryTrace; P0AFG6; -.
DR PRO; PR:P0AFG6; -.
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; IDA:EcoliWiki.
DR GO; GO:0004149; F:dihydrolipoyllysine-residue succinyltransferase activity; IDA:EcoliWiki.
DR GO; GO:0031405; F:lipoic acid binding; IDA:EcoliWiki.
DR GO; GO:0033512; P:L-lysine catabolic process to acetyl-CoA via saccharopine; IEA:UniProtKB-UniPathway.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IDA:ComplexPortal.
DR Gene3D; 3.30.559.10; -; 1.
DR Gene3D; 4.10.320.10; -; 1.
DR InterPro; IPR003016; 2-oxoA_DH_lipoyl-BS.
DR InterPro; IPR001078; 2-oxoacid_DH_actylTfrase.
DR InterPro; IPR000089; Biotin_lipoyl.
DR InterPro; IPR023213; CAT-like_dom_sf.
DR InterPro; IPR036625; E3-bd_dom_sf.
DR InterPro; IPR004167; PSBD.
DR InterPro; IPR011053; Single_hybrid_motif.
DR InterPro; IPR006255; SucB.
DR Pfam; PF00198; 2-oxoacid_dh; 1.
DR Pfam; PF00364; Biotin_lipoyl; 1.
DR Pfam; PF02817; E3_binding; 1.
DR SUPFAM; SSF47005; SSF47005; 1.
DR SUPFAM; SSF51230; SSF51230; 1.
DR TIGRFAMs; TIGR01347; sucB; 1.
DR PROSITE; PS50968; BIOTINYL_LIPOYL; 1.
DR PROSITE; PS00189; LIPOYL; 1.
DR PROSITE; PS51826; PSBD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Acyltransferase; Direct protein sequencing;
KW Lipoyl; Reference proteome; Transferase; Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 2..405
FT /note="Dihydrolipoyllysine-residue succinyltransferase
FT component of 2-oxoglutarate dehydrogenase complex"
FT /id="PRO_0000162262"
FT DOMAIN 3..78
FT /note="Lipoyl-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01066"
FT DOMAIN 113..150
FT /note="Peripheral subunit-binding (PSBD)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01170"
FT REGION 75..111
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 153..178
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 93..111
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 376
FT /evidence="ECO:0000305|PubMed:10739245,
FT ECO:0000305|PubMed:9677295"
FT ACT_SITE 380
FT /evidence="ECO:0000305|PubMed:10739245,
FT ECO:0000305|PubMed:9677295"
FT MOD_RES 44
FT /note="N6-lipoyllysine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01066,
FT ECO:0000269|PubMed:8950276"
FT MOD_RES 148
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:1PMR"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:1PMR"
FT STRAND 70..76
FT /evidence="ECO:0007829|PDB:1PMR"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:1BAL"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:1BAL"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:1BAL"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:1BBL"
FT STRAND 136..139
FT /evidence="ECO:0007829|PDB:2BTH"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:1BAL"
FT TURN 147..149
FT /evidence="ECO:0007829|PDB:1BAL"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:1C4T"
FT HELIX 183..196
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 201..209
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 211..228
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 235..248
FT /evidence="ECO:0007829|PDB:1SCZ"
FT TURN 250..253
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 269..271
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 287..289
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 292..305
FT /evidence="ECO:0007829|PDB:1SCZ"
FT TURN 306..309
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 313..316
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 320..325
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 326..329
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:6PBR"
FT STRAND 343..358
FT /evidence="ECO:0007829|PDB:1SCZ"
FT STRAND 361..375
FT /evidence="ECO:0007829|PDB:1SCZ"
FT TURN 376..378
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 381..396
FT /evidence="ECO:0007829|PDB:1SCZ"
FT HELIX 400..403
FT /evidence="ECO:0007829|PDB:1SCZ"
SQ SEQUENCE 405 AA; 44011 MW; 8439E48C6D381277 CRC64;
MSSVDILVPD LPESVADATV ATWHKKPGDA VVRDEVLVEI ETDKVVLEVP ASADGILDAV
LEDEGTTVTS RQILGRLREG NSAGKETSAK SEEKASTPAQ RQQASLEEQN NDALSPAIRR
LLAEHNLDAS AIKGTGVGGR LTREDVEKHL AKAPAKESAP AAAAPAAQPA LAARSEKRVP
MTRLRKRVAE RLLEAKNSTA MLTTFNEVNM KPIMDLRKQY GEAFEKRHGI RLGFMSFYVK
AVVEALKRYP EVNASIDGDD VVYHNYFDVS MAVSTPRGLV TPVLRDVDTL GMADIEKKIK
ELAVKGRDGK LTVEDLTGGN FTITNGGVFG SLMSTPIINP PQSAILGMHA IKDRPMAVNG
QVEILPMMYL ALSYDHRLID GRESVGFLVT IKELLEDPTR LLLDV
