3FSY

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8052856	3001804	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8052856	3001804	SCOP2B (2022-06-29)
C	SCOP2 Family	Tetrahydrodipicolinate N-succinyltransferase, Mtb-DapD-like	8050591	4006968	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Trimeric LpxA-like enzymes	8052856	3001804	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8052856	3001804	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8052856	3001804	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Hexapep_2	e3fsyA1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
A	THDPS_N	e3fsyA2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
B	Hexapep_2	e3fsyB1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
B	THDPS_N	e3fsyB2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
C	Hexapep_2	e3fsyC1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
C	THDPS_N	e3fsyC2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
D	Hexapep_2	e3fsyD1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
D	THDPS_N	e3fsyD2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
E	Hexapep_2	e3fsyE1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
E	THDPS_N	e3fsyE2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
B	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
B	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
C	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
D	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
D	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
E	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
E	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF14789	Tetrahydrodipicolinate N-succinyltransferase middle (THDPS_M)	Tetrahydrodipicolinate N-succinyltransferase middle	This is the middle domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [1].	Domain
A, B, C, D, E	PF14602	Hexapeptide repeat of succinyl-transferase (Hexapep_2)	Hexapeptide repeat of succinyl-transferase	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Tetrahydrodipicolinate N-succinyltransferase	N-succinyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity succinyltransferase activity catalytic activity N-acyltransferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding N-succinyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity succinyltransferase activity catalytic activity N-acyltransferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding amide binding acyl-CoA binding nucleoside phosphate binding organic cyclic compound binding anion binding succinyl-CoA binding heterocyclic compound binding sulfur compound binding alkali metal ion binding sodium ion binding	diaminopimelate biosynthetic process oxoacid metabolic process cellular biosynthetic process lipid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process small molecule biosynthetic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process diaminopimelate biosynthetic process oxoacid metabolic process cellular biosynthetic process lipid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process small molecule biosynthetic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process fatty acid derivative metabolic process diaminopimelate metabolic process amino acid biosynthetic process biosynthetic process metabolic process cellular process lipid metabolic process lysine metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process alpha-amino acid metabolic process lysine biosynthetic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR001451	Hexapeptide repeat	Repeat
A, B, C, D, E	IPR011004	Trimeric LpxA-like superfamily	Homologous Superfamily
A, B, C, D, E	IPR038361	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR026586	Type 2 tetrahydrodipicolinate N-succinyltransferase family	Family
A, B, C, D, E	IPR019875	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, actinobacteria	Family
A, B, C, D, E	IPR032784	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.