3PB0 | pdb_00003pb0

Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals evolutionary insights

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)
D	d3pb0d1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D	d3pb0d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d3pb0c1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d3pb0c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d3pb0b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d3pb0b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d3pb0a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d3pb0a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Aldolase	8037222	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8037222	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8037222	3000445	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aldolase	8037222	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)
D	Reo_sigma1	e3pb0D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
C	Reo_sigma1	e3pb0C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
B	Reo_sigma1	e3pb0B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
A		e3pb0A1	A: alpha bundles	X: Baculovirus p35 protein-related	H: Bet v1-like	T: Bet v1-like	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	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	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	Dihydrodipicolinate synthase	4-hydroxy-tetrahydrodipicolinate synthase activity amine-lyase activity lyase activity catalytic activity carbon-nitrogen lyase activity	diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process dicarboxylic acid biosynthetic process lipid metabolic process lysine metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process alpha-amino acid metabolic process L-lysine biosynthetic process via diaminopimelate L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.