|Gene:||sucB||Accession Numbers: EG10980 (EcoCyc), b0727, ECK0715|
Synonyms: E2(o) subunit
Component of: 2-oxoglutarate dehydrogenase complex (summary available)
Subunit composition of dihydrolipoyltranssuccinylase = [SucB]24
E. coli SucB is responsible for the dihydrolipoyltranssuccinylase (dihydrolipoamide succinyltransferase) activity of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDHC) that catalyzes the conversion of 2-oxoglutarate (2-ketoglutarate) to succinyl-CoA and carbon dioxide, with the production of NADH (see 2-oxoglutarate decarboxylation to succinyl-CoA). SucB catalyzes the transfer of a succinyl group from the S-succinyldihydrolipoyl moiety to coenzyme A, forming succinyl-CoA.
The OGDHC is a member of the 2-oxo acid dehydrogenase family [Bunik08]. Members of this family contain multiple copies of three enzymatic components: 2-oxoglutarate decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). In most Gram-positive bacteria and in mitochondria the E1 component is a heterodimer composed of two subunits, while in most (but not all) Gram-negative bacteria it is made up of a single type of subunit. In both cases multiple copies of the E1 component along with multiple copies of the E3 component are assembled around an E2 core of 24 subunits with octahedral symmetry, or 60 subunits with eicosahedral symmetry (depending on which complex and species) [Reed01]. In E. coli the E3 component is shared with the pyruvate dehydrogenase and glycine cleavage multi-enzyme complexes. E1 and E2 differ slightly for the 2-oxoglutarate and pyruvate dehydrogenase complexes, and are designated (o) and (p) to distinguish them.
The E. coli OGDHC contains 12 units of the E1(o) component 2-oxoglutarate decarboxylase, thiamine-requiring encoded by sucA, 24 units of the E2(o) component dihydrolipoyltranssuccinylase encoded by sucB, and 2 units of the E3 component lipoamide dehydrogenase encoded by lpd. The 24 E2(o) units form the octahedral core of the complex. They contain lipoyllysine and binding sites for dimers of the E1(o) and E3 subunits. Electron cryotomography showed that they are flexibly tethered to the E2 core [Murphy05].
SucB has a single lipoyl domain at the N-terminus, and a domain with catalytic and subunit binding activity at the C-terminus. It also has areas that contain a large amount of alanine and proline [Spencer84]. The domain structure has been examined by limited proteolysis experiments [Packman87]. Data has suggested that E2(o) has a role in substrate specificity and channeling [Shim11, Perham02]. SucB is lipoylated by LipB, or LplA [Hassan11] (see the reactions below).
The crystal structure of the catalytic domain of SucB provided insights into its interaction with the lipoyl domain [Knapp00, Knapp98]. The crystal structure of the lipoyl domain has also been determined [Ricaud96]. This domain has also been studied by analysis of NMR spectra [Robien92, Ferguson05, Neuweiler09, Jones08].
SucB (E2(o)) has similarity to the AceF (E2(p)) subunit of the pyruvate dehydrogenase multienzyme complex although the N-terminal domain of AceF contains three lipoyl repeats, whereas SucB contains only one of these sequences [Spencer84]. E. coli SucB has similarity to Coxiella burnetii SucB, which elicits an immune response in infected humans [Nguyen99]. The Mycobacterium tuberculosis SucB is involved in a protective antioxidant response to attack by the immune system [Bryk02].
REACTION: E1(o) + TPP = E1(o).TPP, E1(o).TPP + 2-oxoglutarate = E1(o).hydroxycarboxypropylTPP + CO(2), E1(o).hydroxycarboxypropylTPP + E2(o).lipoate(S2) = E1(o).TPP + E2(o).lipoate(SH)(S-succinyl) (see [Waskiewicz84, Steginsky85])
The sucB gene was cloned and sequenced in earlier work [Spencer82, Spencer84] and the initial sequence of the gene was corrected [Packman87]. Transcription of the sucB gene has been analyzed in relation to other members of its gene cluster [Spencer85, Buck85, Buck86, Park97, Cunningham98]. The sucAB and sucCD genes were shown to be mutually essential, with either pair sufficient to produce succinyl-CoA, but simultaneous deletion of sucAB and sucCD was not viable [Yu06]. SucB and SucC were induced during growth at low pH [Stancik02]. Mutant studies showed that the sucB gene is involved in resistance to antibiotics and other stresses in a persister population of E. coli [Ma10].
|Map Position: [760,745 -> 761,962] (16.4 centisomes, 59°)||Length: 1218 bp / 405 aa|
Molecular Weight of Polypeptide: 44.011 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0002480 , CGSC:145 , DIP:DIP-35787N , EchoBASE:EB0973 , EcoGene:EG10980 , EcoliWiki:b0727 , Mint:MINT-1242608 , OU-Microarray:b0727 , PortEco:sucB , PR:PRO_000024003 , Pride:P0AFG6 , Protein Model Portal:P0AFG6 , RegulonDB:EG10980 , SMR:P0AFG6 , String:511145.b0727 , Swiss-Model:P0AFG6 , UniProt:P0AFG6
Relationship Links: InterPro:IN-FAMILY:IPR000089 , InterPro:IN-FAMILY:IPR001078 , InterPro:IN-FAMILY:IPR003016 , InterPro:IN-FAMILY:IPR004167 , InterPro:IN-FAMILY:IPR006255 , InterPro:IN-FAMILY:IPR011053 , InterPro:IN-FAMILY:IPR023213 , PDB:Structure:1BAL , PDB:Structure:1BBL , PDB:Structure:1C4T , PDB:Structure:1E2O , PDB:Structure:1PMR , PDB:Structure:1SCZ , PDB:Structure:1W4H , PDB:Structure:2BTG , PDB:Structure:2BTH , PDB:Structure:2WXC , Pfam:IN-FAMILY:PF00198 , Pfam:IN-FAMILY:PF00364 , Pfam:IN-FAMILY:PF02817 , Prosite:IN-FAMILY:PS00189 , Prosite:IN-FAMILY:PS50968
In Paralogous Gene Group: 39 (2 members)
Reactions known to consume the compound:
Not in pathways:
ATP + SucB + (R)-lipoate → AMP + SucB-lipoate + diphosphate
In Reactions of unknown directionality:
Not in pathways:
SucB + lipoyl-ACP = SucB-lipoate + a holo-[acyl-carrier protein]
Instance reactions of [a [lipoyl-carrier protein] N6-dihydrolipoyl-L-lysine + NAD+ = a [lipoyl-carrier protein] N6-lipoyl-L-lysine + NADH + H+] (184.108.40.206):
|Biological Process:||GO:0006099 - tricarboxylic acid cycle
[UniProtGOA11, GOA01, Spencer82]
GO:0008152 - metabolic process [GOA01]
GO:0033512 - L-lysine catabolic process to acetyl-CoA via saccharopine [UniProtGOA12]
|Molecular Function:||GO:0004149 - dihydrolipoyllysine-residue succinyltransferase activity
[GOA01a, GOA01, Spencer82, Willms67]
GO:0005515 - protein binding [Rajagopala14, Butland05]
GO:0031405 - lipoic acid binding [Packman91]
GO:0016740 - transferase activity [UniProtGOA11]
GO:0016746 - transferase activity, transferring acyl groups [UniProtGOA11, GOA01]
|Cellular Component:||GO:0005829 - cytosol
[DiazMejia09, Ishihama08, Molloy00, LopezCampistrou05]
GO:0045252 - oxoglutarate dehydrogenase complex [GOA01, Willms67]
|MultiFun Terms:||metabolism → energy metabolism, carbon → TCA cycle|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||Yes||37||Aerobic||7||Yes [Baba06, Comment 1]|
|M9 medium with 1% glycerol||Yes||37||Aerobic||7.2||0.35||Yes [Joyce06, Comment 2]|
|MOPS medium with 0.4% glucose||Yes||37||Aerobic||7.2||0.22||Yes [Baba06, Comment 1] |
Yes [Feist07, Comment 3]
Enzymatic reaction of: dihydrolipoyltranssuccinylase
Synonyms: lipoate succinyltransferase, dihydrolipoamide succinyltransferase, lipoamide acyltransferase
EC Number: 220.127.116.11
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.
The reaction is physiologically favored in the direction shown.
In Pathways: 2-oxoglutarate decarboxylation to succinyl-CoA
Subunit of: 2-oxoglutarate dehydrogenase complex
Subunit composition of
2-oxoglutarate dehydrogenase complex = [(SucA)12][(SucB)24][(Lpd)2]
2-oxoglutarate decarboxylase, thiamine-requiring = (SucA)12 (extended summary available)
subunit of E1(0) component of 2-oxoglutarate dehydrogenase = SucA
dihydrolipoyltranssuccinylase = (SucB)24 (extended summary available)
lipoamide dehydrogenase = (Lpd)2 (extended summary available)
E3 monomer = Lpd
The 2-oxoglutarate (2-ketoglutarate) dehydrogenase complex is similar in enzyme composition and complex reactions to the pyruvate dehydrogenase complex reactions [Perham87, Stephens83, Perham89] (see 2-oxoglutarate decarboxylation to succinyl-CoA and pyruvate decarboxylation to acetyl CoA).
SUBREACTIONS: E1(o) + TPP = E1(o).TPP E1(o).TPP + succinate = E1(o).hydroxycarboxypropylTPP + CO(2) E1(o).hydroxycarboxypropylTPP + E2(o).lipoate(S2) = E1(o).TPP + E2(o).lipoate(SH)(S-succinyl) E2(o).lipoate(SH)(S-succinyl) + CoA = E2(o).lip(SH)2 + succinylCoA E3 + FAD = E3.FAD E3.FAD + E2(o).lip(SH)2 = E3.FADH(2) + E2(o).lip(S)2 E3.FADH(2) + NAD(+) = E3.FAD + NADH + H(+) (see [Steginsky85, Waskiewicz84].
Enzymatic reaction of: 2-oxoglutarate dehydrogenase
Synonyms: α-ketoglutarate dehydrogenase, 2-ketoglutarate dehydrogenase
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
The reaction is favored in the direction shown.
In Pathways: 2-oxoglutarate decarboxylation to succinyl-CoA , superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , superpathway of glyoxylate bypass and TCA , TCA cycle I (prokaryotic)
The [Waskiewicz84] data are for E. coli B.
|Chain||2 -> 405|
|Conserved-Region||3 -> 78|
10/20/97 Gene b0727 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10980; confirmed by SwissProt match.
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