|Gene:||sucA||Accession Numbers: EG10979 (EcoCyc), b0726, ECK0714|
Synonyms: lys, lys+met, E1(o) subunit
Component of: 2-oxoglutarate dehydrogenase complex (summary available)
Subunit composition of
2-oxoglutarate decarboxylase, thiamine-requiring = [SucA]12
subunit of E1(0) component of 2-oxoglutarate dehydrogenase = SucA
E. coli SucA is responsible for the 2-oxoglutarate decarboxylase activity of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDHC) that catalyzes the conversion of 2-oxoglutarate (2-ketoglutarate) to succinyl-CoA and CO2, with the production of NADH (see 2-oxoglutarate decarboxylation to 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) comoponent 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].
During the OGDHC reaction cycle, 2-oxoglutarate is bound and decarboxylated by SucA, a thiamin-diphosphate cofactor containing enzyme. The crystal structure of a truncated, apo form of SucA lacking the N-terminal 77 residues has been determined at 2.6 Å resolution. The structure of the holo form with thiamin diphoisphate and Mg2+ was determined at 3.5 Å resolution. The truncated form retained decarboxylase activity but did not assemble with E2(o) into an OGDH complex. Data also suggested the presence of an AMP binding site [Frank07]. An oxygen-dependent thiamin free radical was demonstrated in the OGDHC, which was generated by a side reaction with O2 [Frank08].
Studies of engineered SucA prepared by saturation mutagenesis of His260 and His298 suggested that His260 is required for substrate recognition, but His298 could be replaced by hydrophobic residues of similar size. Data also suggested that E2(o) has a role in specificity [Shim11].
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 sucA gene was cloned and sequenced in earlier work [Spencer82, Darlison84a] and regulation of sucABCD was studied [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].
|Map Position: [757,929 -> 760,730] (16.34 centisomes, 59°)||Length: 2802 bp / 933 aa|
Molecular Weight of Polypeptide: 105.06 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0002478 , CGSC:146 , DIP:DIP-36225N , EchoBASE:EB0972 , EcoGene:EG10979 , EcoliWiki:b0726 , Mint:MINT-1243484 , ModBase:P0AFG3 , OU-Microarray:b0726 , PortEco:sucA , PR:PRO_000024002 , Pride:P0AFG3 , Protein Model Portal:P0AFG3 , RefSeq:NP_415254 , RegulonDB:EG10979 , SMR:P0AFG3 , String:511145.b0726 , UniProt:P0AFG3
Relationship Links: InterPro:IN-FAMILY:IPR001017 , InterPro:IN-FAMILY:IPR005475 , InterPro:IN-FAMILY:IPR011603 , InterPro:IN-FAMILY:IPR029061 , Panther:IN-FAMILY:PTHR23152 , PDB:Structure:2JGD , Pfam:IN-FAMILY:PF00676 , Pfam:IN-FAMILY:PF02779 , Smart:IN-FAMILY:SM00861
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:0006096 - glycolytic process
GO:0006099 - tricarboxylic acid cycle [GOA01, Gaudet10]
GO:0008152 - metabolic process [GOA01]
GO:0055114 - oxidation-reduction process [UniProtGOA11]
|Molecular Function:||GO:0000287 - magnesium ion binding
GO:0004591 - oxoglutarate dehydrogenase (succinyl-transferring) activity [GOA01a, GOA01, Frank07]
GO:0005515 - protein binding [Rajagopala14, Butland05]
GO:0030976 - thiamine pyrophosphate binding [GOA01, Frank07]
GO:0042802 - identical protein binding [Rajagopala14, Lasserre06]
GO:0016491 - oxidoreductase activity [UniProtGOA11]
GO:0016624 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [GOA01]
|Cellular Component:||GO:0005829 - cytosol
[DiazMejia09, Ishihama08, Lasserre06]
GO:0045252 - oxoglutarate dehydrogenase complex [Gaudet10]
|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: 2-oxoglutarate decarboxylase
Synonyms: oxoglutarate oxidoreductase, decarboxylase, 2-ketoglutarate decarboxylase
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
E1(o) activity was analyzed by mixing purified E1(o) enzyme with E2(o) and E3 enzymes in vitro and monitoring the formation of NADH spectrophotometrically [Frank07]. The [Waskiewicz84] data are for E. coli B.
|[Gupta80, BRENDA, 2014]|
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, Stephens83a, 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.
10/20/97 Gene b0726 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10979; confirmed by SwissProt match.
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
Buck89: Buck D, Guest JR (1989). "Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon." Biochem J 1989;260(3);737-47. PMID: 2548486
Bunik08: Bunik VI, Degtyarev D (2008). "Structure-function relationships in the 2-oxo acid dehydrogenase family: substrate-specific signatures and functional predictions for the 2-oxoglutarate dehydrogenase-like proteins." Proteins 71(2);874-90. PMID: 18004749
Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043
Darlison84a: Darlison MG, Spencer ME, Guest JR (1984). "Nucleotide sequence of the sucA gene encoding the 2-oxoglutarate dehydrogenase of Escherichia coli K-12." Eur J Biochem. 141(2):351-9. PMID: 6376123
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909
Frank07: Frank RA, Price AJ, Northrop FD, Perham RN, Luisi BF (2007). "Crystal structure of the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex." J Mol Biol 368(3);639-51. PMID: 17367808
Gupta79: Gupta SC, Dekker EE (1979). "Oxidation of 2-keto-4-hydroxyglutarate by pig heart and Escherichia coli alpha-ketoglutarate dehydrogenase complex." Arch Biochem Biophys 192(1);324-6. PMID: 373631
Gupta80: Gupta SC, Dekker EE (1980). "Evidence for the identity and some comparative properties of alpha-ketoglutarate and 2-keto-4-hydroxyglutarate dehydrogenase activity." J Biol Chem 255(3);1107-12. PMID: 6985904
Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394
Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726
Lindsay00: Lindsay H, Beaumont E, Richards SD, Kelly SM, Sanderson SJ, Price NC, Lindsay JG (2000). "FAD insertion is essential for attaining the assembly competence of the dihydrolipoamide dehydrogenase (E3) monomer from Escherichia coli." J Biol Chem 275(47);36665-70. PMID: 10970889
Magnusson86: Magnusson K, Philips MK, Guest JR, Rutberg L (1986). "Nucleotide sequence of the gene for cytochrome b558 of the Bacillus subtilis succinate dehydrogenase complex." J Bacteriol 1986;166(3);1067-71. PMID: 3086287
Park97: Park SJ, Chao G, Gunsalus RP (1997). "Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter." J Bacteriol 179(13);4138-42. PMID: 9209026
Pettit73: Pettit FH, Hamilton L, Munk P, Namihira G, Eley MH, Willms CR, Reed LJ (1973). "Alpha-keto acid dehydrogenase complexes. XIX. Subunit structure of the Escherichia coli alpha-ketoglutarate dehydrogenase complex." J Biol Chem 248(15);5282-90. PMID: 4588679
Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554
Shim11: Shim da J, Nemeria NS, Balakrishnan A, Patel H, Song J, Wang J, Jordan F, Farinas ET (2011). "Assignment of function to histidines 260 and 298 by engineering the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase complex; substitutions that lead to acceptance of substrates lacking the 5-carboxyl group." Biochemistry 50(35);7705-9. PMID: 21809826
Steginsky85: Steginsky CA, Gruys KJ, Frey PA (1985). "alpha-Ketoglutarate dehydrogenase complex of Escherichia coli. A hybrid complex containing pyruvate dehydrogenase subunits from pyruvate dehydrogenase complex." J Biol Chem 260(25);13690-3. PMID: 3902822
Stephens83a: Stephens PE, Darlison MG, Lewis HM, Guest JR (1983). "The pyruvate dehydrogenase complex of Escherichia coli K12. Nucleotide sequence encoding the dihydrolipoamide acetyltransferase component." Eur J Biochem 1983;133(3);481-9. PMID: 6345153
Waskiewicz84: Waskiewicz DE, Hammes GG (1984). "Elementary steps in the reaction mechanism of the alpha-ketoglutarate dehydrogenase multienzyme complex from Escherichia coli: kinetics of succinylation and desuccinylation." Biochemistry 23(14);3136-43. PMID: 6380583
Wood84: Wood D, Darlison MG, Wilde RJ, Guest JR (1984). "Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli." Biochem J 1984;222(2);519-34. PMID: 6383359
Iuchi88: Iuchi S, Lin EC (1988). "arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways." Proc Natl Acad Sci U S A 1988;85(6);1888-92. PMID: 2964639
Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324
Lynch96: Lynch AS, Lin EC (1996). "Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters." J Bacteriol 1996;178(21);6238-49. PMID: 8892825
Marzan et al., 2013: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360
Park95: Park SJ, Tseng CP, Gunsalus RP (1995). "Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr." Mol Microbiol 15(3);473-82. PMID: 7783618
Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038
Shen97: Shen J, Gunsalus RP (1997). "Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli." Mol Microbiol 26(2);223-36. PMID: 9383149
Trotter11: Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J (2011). "Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment." PLoS One 6(9);e25501. PMID: 21980479
Wright13: Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs." Proc Natl Acad Sci U S A 110(37);E3487-96. PMID: 23980183
Zhang05: Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH (2005). "Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli." J Bacteriol 187(3);980-90. PMID: 15659676
Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470
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