ODO2_AZOVI
ID ODO2_AZOVI Reviewed; 399 AA.
AC P20708; Q44474;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 25-MAY-2022, entry version 128.
DE RecName: Full=Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex;
DE EC=2.3.1.61 {ECO:0000250|UniProtKB:P0AFG6};
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; Synonyms=odhB;
OS Azotobacter vinelandii.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Azotobacter.
OX NCBI_TaxID=354;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 478 / DSM 2289 / BCRC 14361 / JCM 21475 / KCTC 12137 / NBRC
RC 102612 / NCIMB 12096 / NRRL B-14641 / VKM B-1617 / NRS 16;
RX PubMed=2404760; DOI=10.1111/j.1432-1033.1990.tb15300.x;
RA Westphal A.H., de Kok A.;
RT "The 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. 2.
RT Molecular cloning and sequence analysis of the gene encoding the
RT succinyltransferase component.";
RL Eur. J. Biochem. 187:235-239(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 354-399.
RC STRAIN=ATCC 478 / DSM 2289 / BCRC 14361 / JCM 21475 / KCTC 12137 / NBRC
RC 102612 / NCIMB 12096 / NRRL B-14641 / VKM B-1617 / NRS 16;
RX PubMed=2832161; DOI=10.1111/j.1432-1033.1988.tb13887.x;
RA Westphal A.H., de Kok A.;
RT "Lipoamide dehydrogenase from Azotobacter vinelandii. Molecular cloning,
RT organization and sequence analysis of the gene.";
RL Eur. J. Biochem. 172:299-305(1988).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-30.
RC STRAIN=ATCC 478 / DSM 2289 / BCRC 14361 / JCM 21475 / KCTC 12137 / NBRC
RC 102612 / NCIMB 12096 / NRRL B-14641 / VKM B-1617 / NRS 16;
RX PubMed=2404759; DOI=10.1111/j.1432-1033.1990.tb15299.x;
RA Schulze E., Westphal A.H., Hanemaaijer R., de Kok A.;
RT "The 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. 1.
RT Molecular cloning and sequence analysis of the gene encoding the 2-
RT oxoglutarate dehydrogenase component.";
RL Eur. J. Biochem. 187:229-234(1990).
RN [4]
RP STRUCTURE BY NMR OF 1-80.
RX PubMed=8529634; DOI=10.1111/j.1432-1033.1995.148_c.x;
RA Berg A., Smits O., de Kok A., Vervoort J.;
RT "Sequential 1H and 15N nuclear magnetic resonance assignments and secondary
RT structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex
RT from Azotobacter vinelandii. Evidence for high structural similarity with
RT the lipoyl domain of the pyruvate dehydrogenase complex.";
RL Eur. J. Biochem. 234:148-159(1995).
RN [5]
RP STRUCTURE BY NMR OF 1-78.
RX PubMed=8780784; DOI=10.1006/jmbi.1996.0474;
RA Berg A., Vervoort J., de Kok A.;
RT "Solution structure of the lipoyl domain of the 2-oxoglutarate
RT dehydrogenase complex from Azotobacter vinelandii.";
RL J. Mol. Biol. 261:432-442(1996).
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:0000250|UniProtKB:P0AFG6}.
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:0000250|UniProtKB:P0AFG6};
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. Part of the 2-oxoglutarate dehydrogenase (OGDH) complex
CC composed of E1 (2-oxoglutarate dehydrogenase), E2 (dihydrolipoamide
CC succinyltransferase) and E3 (dihydrolipoamide dehydrogenase); the
CC complex contains multiple copies of the three enzymatic components (E1,
CC E2 and E3). {ECO:0000250|UniProtKB:P0AFG6}.
CC -!- SIMILARITY: Belongs to the 2-oxoacid dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; M37307; AAA22138.1; ALT_SEQ; Genomic_DNA.
DR EMBL; X52432; CAA36678.1; -; Genomic_DNA.
DR EMBL; X52433; CAA36681.1; -; Genomic_DNA.
DR PIR; S07779; S07779.
DR PDB; 1GHJ; NMR; -; A=2-80.
DR PDB; 1GHK; NMR; -; A=2-80.
DR PDBsum; 1GHJ; -.
DR PDBsum; 1GHK; -.
DR AlphaFoldDB; P20708; -.
DR SMR; P20708; -.
DR PRIDE; P20708; -.
DR BRENDA; 2.3.1.61; 49.
DR SABIO-RK; P20708; -.
DR UniPathway; UPA00868; UER00840.
DR EvolutionaryTrace; P20708; -.
DR GO; GO:0045252; C:oxoglutarate dehydrogenase complex; IEA:InterPro.
DR GO; GO:0004149; F:dihydrolipoyllysine-residue succinyltransferase activity; IEA:UniProtKB-EC.
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; IEA:UniProtKB-KW.
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; Acyltransferase; Lipoyl; Transferase;
KW Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..399
FT /note="Dihydrolipoyllysine-residue succinyltransferase
FT component of 2-oxoglutarate dehydrogenase complex"
FT /id="PRO_0000162255"
FT DOMAIN 2..77
FT /note="Lipoyl-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01066"
FT DOMAIN 104..141
FT /note="Peripheral subunit-binding (PSBD)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01170"
FT ACT_SITE 370
FT /evidence="ECO:0000250|UniProtKB:P0AFG6"
FT ACT_SITE 374
FT /evidence="ECO:0000250|UniProtKB:P0AFG6"
FT MOD_RES 43
FT /note="N6-lipoyllysine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01066"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:1GHJ"
FT STRAND 17..19
FT /evidence="ECO:0007829|PDB:1GHJ"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:1GHJ"
FT STRAND 35..40
FT /evidence="ECO:0007829|PDB:1GHJ"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:1GHJ"
FT STRAND 54..61
FT /evidence="ECO:0007829|PDB:1GHJ"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:1GHJ"
SQ SEQUENCE 399 AA; 42003 MW; 3A801A1B519E73D3 CRC64;
MAIDIKAPTF PESIADGTVA TWHKKPGEPV KRDELIVDIE TDKVVMEVLA EADGVIAEIV
KNEGDTVLSG ELLGKLTEGG AATAAPAAAP APAAAAPAAA EAPILSPAAR KIAEENAIAA
DSITGTGKGG RVTKEDAVAA AEAKKSAPAG QPAPAATAAP LFAAGDRVEK RVPMTRLRAK
VAERLVEAQS SMAMLTTFNE VNMKPVMELR AKYKDLFEKT HNGVRLGFMS FFVKAAVEAL
KRQPGVNASI DGNDIVYHGY QDIGVAVSSD RGLVVPVLRN AEFMSLAEIE GGINEFGKKA
KAGKLTIEEM TGGTFTISNG GVFGSLLSTP IVNPPQTAIL GMHKIQERPM AVNGQVVILP
MMYLALSYDH RLIDGKEAVT FLVTMKDLLE DPARLLLDV
