1XXX

Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xxxa1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1xxxb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1xxxc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1xxxd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E	d1xxxe_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
F	d1xxxf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
G	d1xxxg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
H	d1xxxh_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Dihydrodipicolinate synthase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Class I aldolase	8021568	4003216	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8033948	3000445	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8033948	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8033948	3000445	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aldolase	8033948	3000445	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Aldolase	8033948	3000445	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Aldolase	8033948	3000445	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Aldolase	8033948	3000445	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Aldolase	8033948	3000445	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	PF00701	e1xxxA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
B	PF00701	e1xxxB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
C	PF00701	e1xxxC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
D	PF00701	e1xxxD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
E	PF00701	e1xxxE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
F	PF00701	e1xxxF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
G	PF00701	e1xxxG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)
H	PF00701	e1xxxH1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00701	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00701	Dihydrodipicolinate synthetase family (DHDPS)	Dihydrodipicolinate synthetase family	This family has a TIM barrel structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Dihydrodipicolinate synthase	4-hydroxy-tetrahydrodipicolinate synthase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	diaminopimelate biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process lipid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process organonitrogen compound metabolic process diaminopimelate biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process lipid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process organonitrogen compound metabolic 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020624	Schiff base-forming aldolase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005263	4-hydroxy-tetrahydrodipicolinate synthase, DapA	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020625	Schiff base-forming aldolase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002220	DapA-like	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.