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Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (EC 2.3.1.61) (2-oxoglutarate dehydrogenase complex component E2) (OGDC-E2) (Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex)

 ODO2_ECOLI              Reviewed;         405 AA.
P0AFG6; P07016;
01-APR-1988, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
25-OCT-2017, entry version 117.
RecName: Full=Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex;
EC=2.3.1.61;
AltName: Full=2-oxoglutarate dehydrogenase complex component E2;
Short=OGDC-E2;
AltName: Full=Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex;
Name=sucB; OrderedLocusNames=b0727, JW0716;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=6376124; DOI=10.1111/j.1432-1033.1984.tb08200.x;
Spencer M.E., Darlison M.G., Stephens P.E., Duckenfield I.K.,
Guest J.R.;
"Nucleotide sequence of the sucB gene encoding the dihydrolipoamide
succinyltransferase of Escherichia coli K12 and homology with the
corresponding acetyltransferase.";
Eur. J. Biochem. 141:361-374(1984).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8905232; DOI=10.1093/dnares/3.3.137;
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
Yano M., Horiuchi T.;
"A 718-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 12.7-28.0 min region on the linkage map.";
DNA Res. 3:137-155(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
PROTEIN SEQUENCE OF 4-10.
STRAIN=K12;
PubMed=17895580; DOI=10.1266/ggs.82.291;
Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
"A role of RnlA in the RNase LS activity from Escherichia coli.";
Genes Genet. Syst. 82:291-299(2007).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-12.
PubMed=6376123; DOI=10.1111/j.1432-1033.1984.tb08199.x;
Darlison M.G., Spencer M.E., Guest J.R.;
"Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate
dehydrogenase of Escherichia coli K12.";
Eur. J. Biochem. 141:351-359(1984).
[7]
PROTEIN SEQUENCE OF 2-13.
STRAIN=K12 / EMG2;
PubMed=9298646; DOI=10.1002/elps.1150180807;
Link A.J., Robison K., Church G.M.;
"Comparing the predicted and observed properties of proteins encoded
in the genome of Escherichia coli K-12.";
Electrophoresis 18:1259-1313(1997).
[8]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[9]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-148, AND IDENTIFICATION BY
MASS SPECTROMETRY.
STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
PubMed=18723842; DOI=10.1074/mcp.M800187-MCP200;
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
Grishin N.V., Zhao Y.;
"Lysine acetylation is a highly abundant and evolutionarily conserved
modification in Escherichia coli.";
Mol. Cell. Proteomics 8:215-225(2009).
[10]
STRUCTURE BY NMR OF 1-81, AND LIPOYLATION AT LYS-44.
PubMed=8950276; DOI=10.1006/jmbi.1996.0632;
Ricaud P.M., Howard M.J., Roberts E.L., Broadhurst R.W., Perham R.N.;
"Three-dimensional structure of the lipoyl domain from the
dihydrolipoyl succinyltransferase component of the 2-oxoglutarate
dehydrogenase multienzyme complex of Escherichia coli.";
J. Mol. Biol. 264:179-190(1996).
[11]
STRUCTURE BY NMR OF 104-153.
PubMed=1554728; DOI=10.1021/bi00128a021;
Robien M.A., Clore G.M., Omichinski J.G., Perham R.N., Appella E.,
Sakaguchi K., Gronenborn A.M.;
"Three-dimensional solution structure of the E3-binding domain of the
dihydrolipoamide succinyltransferase core from the 2-oxoglutarate
dehydrogenase multienzyme complex of Escherichia coli.";
Biochemistry 31:3463-3471(1992).
[12]
X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405.
PubMed=9677295; DOI=10.1006/jmbi.1998.1924;
Knapp J.E., Mitchell D.T., Yazdi M.A., Ernst S.R., Reed L.J.,
Hackert M.L.;
"Crystal structure of the truncated cubic core component of the
Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex.";
J. Mol. Biol. 280:655-668(1998).
[13]
X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 173-405.
PubMed=10739245; DOI=10.1110/ps.9.1.37;
Knapp J.E., Carroll D., Lawson J.E., Ernst S.R., Reed L.J.,
Hackert M.L.;
"Expression, purification, and structural analysis of the trimeric
form of the catalytic domain of the Escherichia coli dihydrolipoamide
succinyltransferase.";
Protein Sci. 9:37-48(2000).
-!- FUNCTION: The 2-oxoglutarate dehydrogenase complex catalyzes the
overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It
contains multiple copies of three enzymatic components: 2-
oxoglutarate dehydrogenase (E1), dihydrolipoamide
succinyltransferase (E2) and lipoamide dehydrogenase (E3).
-!- CATALYTIC ACTIVITY: Succinyl-CoA + enzyme N(6)-
(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-
succinyldihydrolipoyl)lysine.
-!- COFACTOR:
Name=(R)-lipoate; Xref=ChEBI:CHEBI:83088;
Note=Binds 1 lipoyl cofactor covalently.;
-!- PATHWAY: Amino-acid degradation; L-lysine degradation via
saccharopine pathway; glutaryl-CoA from L-lysine: step 6/6.
-!- SUBUNIT: Forms a 24-polypeptide structural core with octahedral
symmetry.
-!- INTERACTION:
P0A9P0:lpdA; NbExp=3; IntAct=EBI-558621, EBI-542856;
P0AFG3:sucA; NbExp=7; IntAct=EBI-558621, EBI-543523;
P77717:ybaY; NbExp=3; IntAct=EBI-558621, EBI-558645;
-!- SIMILARITY: Belongs to the 2-oxoacid dehydrogenase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; J01619; AAA23898.1; -; Genomic_DNA.
EMBL; X00664; CAA25284.1; -; Genomic_DNA.
EMBL; U00096; AAC73821.1; -; Genomic_DNA.
EMBL; AP009048; BAA35393.1; -; Genomic_DNA.
EMBL; X00661; CAA25281.1; -; Genomic_DNA.
PIR; F64808; XUECSD.
RefSeq; NP_415255.1; NC_000913.3.
RefSeq; WP_000099823.1; NZ_LN832404.1.
PDB; 1BAL; NMR; -; A=104-153.
PDB; 1BBL; NMR; -; A=104-153.
PDB; 1C4T; X-ray; 3.00 A; A/B/C=173-405.
PDB; 1E2O; X-ray; 3.00 A; A=173-405.
PDB; 1PMR; NMR; -; A=2-81.
PDB; 1SCZ; X-ray; 2.20 A; A=173-405.
PDB; 1W4H; NMR; -; A=109-153.
PDB; 2BTG; NMR; -; A=109-153.
PDB; 2BTH; NMR; -; A=109-153.
PDB; 2WXC; NMR; -; A=109-153.
PDBsum; 1BAL; -.
PDBsum; 1BBL; -.
PDBsum; 1C4T; -.
PDBsum; 1E2O; -.
PDBsum; 1PMR; -.
PDBsum; 1SCZ; -.
PDBsum; 1W4H; -.
PDBsum; 2BTG; -.
PDBsum; 2BTH; -.
PDBsum; 2WXC; -.
ProteinModelPortal; P0AFG6; -.
SMR; P0AFG6; -.
BioGrid; 4259945; 11.
DIP; DIP-35787N; -.
IntAct; P0AFG6; 39.
MINT; MINT-1242608; -.
STRING; 316385.ECDH10B_0793; -.
iPTMnet; P0AFG6; -.
SWISS-2DPAGE; P0AFG6; -.
PaxDb; P0AFG6; -.
PRIDE; P0AFG6; -.
EnsemblBacteria; AAC73821; AAC73821; b0727.
EnsemblBacteria; BAA35393; BAA35393; BAA35393.
GeneID; 945307; -.
KEGG; ecj:JW0716; -.
KEGG; eco:b0727; -.
PATRIC; fig|1411691.4.peg.1546; -.
EchoBASE; EB0973; -.
EcoGene; EG10980; sucB.
eggNOG; ENOG4105C7S; Bacteria.
eggNOG; COG0508; LUCA.
HOGENOM; HOG000281563; -.
InParanoid; P0AFG6; -.
KO; K00658; -.
PhylomeDB; P0AFG6; -.
BioCyc; EcoCyc:E2O-MONOMER; -.
BioCyc; MetaCyc:E2O-MONOMER; -.
BRENDA; 2.3.1.61; 2026.
UniPathway; UPA00868; UER00840.
EvolutionaryTrace; P0AFG6; -.
PRO; PR:P0AFG6; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0045252; C:oxoglutarate dehydrogenase complex; IDA:EcoliWiki.
GO; GO:0004149; F:dihydrolipoyllysine-residue succinyltransferase activity; IDA:EcoliWiki.
GO; GO:0031405; F:lipoic acid binding; IDA:EcoliWiki.
GO; GO:0033512; P:L-lysine catabolic process to acetyl-CoA via saccharopine; IEA:UniProtKB-UniPathway.
GO; GO:0006099; P:tricarboxylic acid cycle; IMP:EcoliWiki.
Gene3D; 4.10.320.10; -; 1.
InterPro; IPR003016; 2-oxoA_DH_lipoyl-BS.
InterPro; IPR001078; 2-oxoacid_DH_actylTfrase.
InterPro; IPR000089; Biotin_lipoyl.
InterPro; IPR004167; E3-bd.
InterPro; IPR036625; E3-bd_dom_sf.
InterPro; IPR011053; Single_hybrid_motif.
InterPro; IPR006255; SucB.
Pfam; PF00198; 2-oxoacid_dh; 1.
Pfam; PF00364; Biotin_lipoyl; 1.
Pfam; PF02817; E3_binding; 1.
SUPFAM; SSF47005; SSF47005; 1.
SUPFAM; SSF51230; SSF51230; 1.
TIGRFAMs; TIGR01347; sucB; 1.
PROSITE; PS50968; BIOTINYL_LIPOYL; 1.
PROSITE; PS00189; LIPOYL; 1.
PROSITE; PS51826; PSBD; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Acyltransferase; Complete proteome;
Direct protein sequencing; Lipoyl; Reference proteome; Transferase;
Tricarboxylic acid cycle.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:9298646}.
CHAIN 2 405 Dihydrolipoyllysine-residue
succinyltransferase component of 2-
oxoglutarate dehydrogenase complex.
/FTId=PRO_0000162262.
DOMAIN 3 78 Lipoyl-binding. {ECO:0000255|PROSITE-
ProRule:PRU01066}.
DOMAIN 113 150 Peripheral subunit-binding (PSBD).
{ECO:0000255|PROSITE-ProRule:PRU01170}.
ACT_SITE 376 376
ACT_SITE 380 380
MOD_RES 44 44 N6-lipoyllysine. {ECO:0000255|PROSITE-
ProRule:PRU01066,
ECO:0000269|PubMed:8950276}.
MOD_RES 148 148 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
STRAND 31 34 {ECO:0000244|PDB:1PMR}.
STRAND 42 44 {ECO:0000244|PDB:1PMR}.
STRAND 70 76 {ECO:0000244|PDB:1PMR}.
STRAND 105 107 {ECO:0000244|PDB:1BAL}.
HELIX 116 118 {ECO:0000244|PDB:1BAL}.
HELIX 121 124 {ECO:0000244|PDB:1BAL}.
HELIX 129 131 {ECO:0000244|PDB:1BBL}.
STRAND 136 139 {ECO:0000244|PDB:2BTH}.
HELIX 143 146 {ECO:0000244|PDB:1BAL}.
TURN 147 149 {ECO:0000244|PDB:1BAL}.
STRAND 176 178 {ECO:0000244|PDB:1C4T}.
HELIX 183 196 {ECO:0000244|PDB:1SCZ}.
STRAND 201 209 {ECO:0000244|PDB:1SCZ}.
HELIX 211 228 {ECO:0000244|PDB:1SCZ}.
HELIX 235 248 {ECO:0000244|PDB:1SCZ}.
TURN 250 253 {ECO:0000244|PDB:1SCZ}.
STRAND 255 257 {ECO:0000244|PDB:1SCZ}.
STRAND 260 262 {ECO:0000244|PDB:1SCZ}.
STRAND 269 271 {ECO:0000244|PDB:1SCZ}.
STRAND 273 275 {ECO:0000244|PDB:1SCZ}.
STRAND 278 280 {ECO:0000244|PDB:1SCZ}.
HELIX 287 289 {ECO:0000244|PDB:1SCZ}.
HELIX 292 305 {ECO:0000244|PDB:1SCZ}.
TURN 306 309 {ECO:0000244|PDB:1SCZ}.
HELIX 313 316 {ECO:0000244|PDB:1SCZ}.
STRAND 320 325 {ECO:0000244|PDB:1SCZ}.
HELIX 326 329 {ECO:0000244|PDB:1SCZ}.
STRAND 343 358 {ECO:0000244|PDB:1SCZ}.
STRAND 361 375 {ECO:0000244|PDB:1SCZ}.
TURN 376 378 {ECO:0000244|PDB:1SCZ}.
HELIX 381 396 {ECO:0000244|PDB:1SCZ}.
HELIX 400 403 {ECO:0000244|PDB:1SCZ}.
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


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