DB code: T00223

RLCP classification	3.1177.805.87 : Transfer
CATH domain	2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
	4.10.320.10 : Dihydrolipoamide Transferase
	3.30.559.10 : Chloramphenicol Acetyltransferase	Catalytic domain
E.C.	2.3.1.61
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)	M00163 M00222 M00145 M00188 M00189 M00190 M00191 M00208
3.30.559.10 : Chloramphenicol Acetyltransferase	M00188 M00189 M00190 M00191
4.10.320.10 : Dihydrolipoamide Transferase	M00188 M00189 M00190 M00191

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P0AFG6	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex	E2 EC 2.3.1.61 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex	NP_415255.1 (Protein) NC_000913.2 (DNA/RNA sequence) YP_489006.1 (Protein) NC_007779.1 (DNA/RNA sequence)	PF00198 (2-oxoacid_dh) PF00364 (Biotin_lipoyl) PF02817 (E3_binding) [Graphical View]
P20708	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex	E2 EC 2.3.1.61 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex		PF00198 (2-oxoacid_dh) PF00364 (Biotin_lipoyl) PF02817 (E3_binding) [Graphical View]

KEGG enzyme name
dihydrolipoyllysine-residue succinyltransferase dihydrolipoamide S-succinyltransferase dihydrolipoamide succinyltransferase dihydrolipoic transsuccinylase dihydrolipolyl transsuccinylase dihydrolipoyl transsuccinylase lipoate succinyltransferase (Escherichia coli) lipoic transsuccinylase lipoyl transsuccinylase succinyl-CoA:dihydrolipoamide S-succinyltransferase succinyl-CoA:dihydrolipoate S-succinyltransferase enzyme-dihydrolipoyllysine:succinyl-CoA S-succinyltransferase

KEGG enzyme name

dihydrolipoyllysine-residue succinyltransferase
dihydrolipoamide S-succinyltransferase
dihydrolipoamide succinyltransferase
dihydrolipoic transsuccinylase
dihydrolipolyl transsuccinylase
dihydrolipoyl transsuccinylase
lipoate succinyltransferase (Escherichia coli)
lipoic transsuccinylase
lipoyl transsuccinylase
succinyl-CoA:dihydrolipoamide S-succinyltransferase
succinyl-CoA:dihydrolipoate S-succinyltransferase
enzyme-dihydrolipoyllysine:succinyl-CoA S-succinyltransferase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P0AFG6	ODO2_ECOLI	Succinyl-CoA + enzyme N(6)- (dihydrolipoyl)lysine = CoA + enzyme N(6)-(S- succinyldihydrolipoyl)lysine.	Forms a 24-polypeptide structural core with octahedral symmetry.		Binds 1 lipoyl cofactor covalently.
P20708	ODO2_AZOVI	Succinyl-CoA + enzyme N(6)- (dihydrolipoyl)lysine = CoA + enzyme N(6)-(S- succinyldihydrolipoyl)lysine.	Forms a 24-polypeptide structural core with octahedral symmetry.		Binds 1 lipoyl cofactor covalently.

KEGG Pathways
Map code	Pathways	E.C.
MAP00020	Citrate cycle (TCA cycle)
MAP00310	Lysine degradation

Compound table
	Substrates		Products		Intermediates
KEGG-id	C00010	C01169	C00091	C00579
E.C.
Compound	CoA	S-Succinyldihydrolipoamide	Succinyl-CoA	Dihydrolipoamide
Type	amine group,carbohydrate,nucleotide ,peptide/protein,sulfhydryl group	amide group,carbohydrate,carboxyl group,lipid,sulfhydryl group,sulfide group	amine group,carbohydrate,carboxyl group,nucleotide ,peptide/protein,sulfide group	amide group,lipid,sulfhydryl group
ChEBI	15346 15346	17432 17432	15380 15380	17694 17694
PubChem	6816 87642 6816 87642	11953795 11953795	439161 92133 439161 92133	663 663

1ghjA	Unbound	Unbound	Unbound	Unbound
1ghkA	Unbound	Unbound	Unbound	Unbound
1pmrA	Unbound	Unbound	Unbound	Unbound
1balA	Unbound	Unbound	Unbound	Unbound
1bblA	Unbound	Unbound	Unbound	Unbound
1w4hA	Unbound	Unbound	Unbound	Unbound
2btgA	Unbound	Unbound	Unbound	Unbound
2bthA	Unbound	Unbound	Unbound	Unbound
1c4tA	Unbound	Unbound	Unbound	Unbound
1c4tB	Unbound	Unbound	Unbound	Unbound
1c4tC	Unbound	Unbound	Unbound	Unbound
1e2oA	Unbound	Unbound	Unbound	Unbound
1sczA	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
Swiss-prot

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1ghjA
1ghkA
1pmrA
1balA
1bblA
1w4hA
2btgA
2bthA
1c4tA	ARG 184;THR 323;HIS 375;ASP 379			HIS 375
1c4tB	ARG 184;THR 323;HIS 375;ASP 379			HIS 375
1c4tC	ARG 184;THR 323;HIS 375;ASP 379			HIS 375
1e2oA	ARG 184;THR 323;HIS 375;ASP 379			HIS 375
1sczA	ARG 184;THR 323;HIS 375;ASP 379			HIS 375

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[9]	p.660-662
[11]	p.41-42

References
[1]
Resource
Comments
Medline ID
PubMed ID	6341609
Journal	J Mol Biol
Year	1983
Volume	165
Pages	523-41
Authors	Wagenknecht T, Francis N, DeRosier DJ
Title	alpha-Ketoglutarate dehydrogenase complex may be heterogeneous in quaternary structure.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	6403946
Journal	Proc Natl Acad Sci U S A
Year	1983
Volume	80
Pages	2226-30
Authors	Hackert ML, Oliver RM, Reed LJ
Title	Evidence for a multiple random coupling mechanism in the alpha-ketoglutarate dehydrogenase multienzyme complex of Escherichia coli: a computer model analysis.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	6376124
Journal	Eur J Biochem
Year	1984
Volume	141
Pages	361-74
Authors	Spencer ME, Darlison MG, Stephens PE, Duckenfield IK, Guest JR
Title	Nucleotide sequence of the sucB gene encoding the dihydrolipoamide succinyltransferase of Escherichia coli K12 and homology with the corresponding acetyltransferase.
Related PDB	1bal 1bbl
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	6380587
Journal	Biochemistry
Year	1984
Volume	23
Pages	3383-9
Authors	Wagenknecht T, Frank J
Title	Localization of lipoyl-bearing domains in the alpha-ketoglutarate dehydrogenase multienzyme complex.
Related PDB
Related UniProtKB
[5]
Resource
Comments	STRUCTURE BY NMR OF 103-152STRUCTURE BY NMR OF 103-152
Medline ID	92207970
PubMed ID	1554728
Journal	Biochemistry
Year	1992
Volume	31
Pages	3463-71
Authors	Robien MA, Clore GM, Omichinski JG, Perham RN, Appella E, Sakaguchi K, Gronenborn AM
Title	Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli.
Related PDB
Related UniProtKB	P0AFG6
[6]
Resource
Comments	STRUCTURE BY NMR OF 1-79.
Medline ID	96096733
PubMed ID	8529634
Journal	Eur J Biochem
Year	1995
Volume	234
Pages	148-59
Authors	Berg A, Smits O, de Kok A, Vervoort J
Title	Sequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. Evidence for high structural similarity with the lipoyl domain of the pyruvate dehydrogenase complex.
Related PDB
Related UniProtKB	P20708
[7]
Resource
Comments	STRUCTURE BY NMR OF 1-77.
Medline ID	96374493
PubMed ID	8780784
Journal	J Mol Biol
Year	1996
Volume	261
Pages	432-42
Authors	Berg A, Vervoort J, de Kok A
Title	Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii.
Related PDB	1ghj 1ghk
Related UniProtKB	P20708
[8]
Resource
Comments	STRUCTURE BY NMR OF 1-80
Medline ID	97107536
PubMed ID	8950276
Journal	J Mol Biol
Year	1996
Volume	264
Pages	179-90
Authors	Ricaud PM, Howard MJ, Roberts EL, Broadhurst RW, Perham RN
Title	Three-dimensional structure of the lipoyl domain from the dihydrolipoyl succinyltransferase component of the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli.
Related PDB	1pmr
Related UniProtKB	P0AFG6
[9]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 172-404
Medline ID	98344105
PubMed ID	9677295
Journal	J Mol Biol
Year	1998
Volume	280
Pages	655-68
Authors	Knapp JE, Mitchell DT, Yazdi MA, Ernst SR, Reed LJ, Hackert ML
Title	Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex.
Related PDB	1e2o
Related UniProtKB	P0AFG6
[10]
Resource
Comments
Medline ID
PubMed ID	10806400
Journal	Eur J Biochem
Year	2000
Volume	267
Pages	3005-16
Authors	Koike K, Suematsu T, Ehara M
Title	Cloning, overexpression and mutagenesis of cDNA encoding dihydrolipoamide succinyltransferase component of the porcine 2-oxoglutarate dehydrogenase complex.
Related PDB
Related UniProtKB
[11]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 172-404
Medline ID	20201852
PubMed ID	10739245
Journal	Protein Sci
Year	2000
Volume	9
Pages	37-48
Authors	Knapp JE, Carroll D, Lawson JE, Ernst SR, Reed LJ, Hackert ML
Title	Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase.
Related PDB	1c4t
Related UniProtKB	P0AFG6
[12]
Resource
Comments
Medline ID
PubMed ID	12481137
Journal	Science
Year	2002
Volume	298
Pages	2191-5
Authors	Garcia-Mira MM, Sadqi M, Fischer N, Sanchez-Ruiz JM, Munoz V
Title	Experimental identification of downhill protein folding.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID	16168437
Journal	J Mol Biol
Year	2005
Volume	353
Pages	427-46
Authors	Ferguson N, Sharpe TD, Schartau PJ, Sato S, Allen MD, Johnson CM, Rutherford TJ, Fersht AR
Title	Ultra-fast barrier-limited folding in the peripheral subunit-binding domain family.
Related PDB	1w4e 1w4f 1w4g 1w4h 2btg 2bth
Related UniProtKB

Comments
PDB structures, 1ghj, 1ghk & 1pmr, correspond to the first domain of this enzyme, lipoyl domain, the other structures, 1bal & 1bbl, comprises the second domain, E3-binding domain, and the rest of structures, 1c4t & 1e2o, are the third domain, catalytic one. According to the literature [9] & [11], the reaction proceeds as follows: (1) His375 acts as a general base to abstract a proton from the acceptor group, thiol group of CoA. (2) Asp379 is thought to modulate the catalytic histidine, His375, by interacting with the residue and Arg184 ([9] & [11]). (Here, the mainchain carbonyl oxygen of His375 might modulate its own sidechain. see M00189 in EzCatDB) (3) The activated thiolate makes a nucleophilic attack on the transferred group, carbonyl carbon atom of the succinylated substrate, resulting in the formation of a tetrahedral intermediate. (4) This intermediate is stabilized by the hydroxyl group of Thr323' from the next subunit (3-fold-related subunit). (5) The breakdown of this intermediate results in the transfer of the succinyl group to CoA and protonation of the dihydrolipoyl group (see [9] & [11]). (His375 can be involved in this protonation.)

Comments

PDB structures, 1ghj, 1ghk & 1pmr, correspond to the first domain of this enzyme, lipoyl domain, the other structures, 1bal & 1bbl, comprises the second domain, E3-binding domain, and the rest of structures, 1c4t & 1e2o, are the third domain, catalytic one.
According to the literature [9] & [11], the reaction proceeds as follows:
(1) His375 acts as a general base to abstract a proton from the acceptor group, thiol group of CoA.
(2) Asp379 is thought to modulate the catalytic histidine, His375, by interacting with the residue and Arg184 ([9] & [11]). (Here, the mainchain carbonyl oxygen of His375 might modulate its own sidechain. see M00189 in EzCatDB)
(3) The activated thiolate makes a nucleophilic attack on the transferred group, carbonyl carbon atom of the succinylated substrate, resulting in the formation of a tetrahedral intermediate.
(4) This intermediate is stabilized by the hydroxyl group of Thr323' from the next subunit (3-fold-related subunit).
(5) The breakdown of this intermediate results in the transfer of the succinyl group to CoA and protonation of the dihydrolipoyl group (see [9] & [11]). (His375 can be involved in this protonation.)

Created	Updated
2002-12-03	2009-09-29