1ARZ

ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1arza1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d1arza2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1arzb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1arzb2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1arzc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1arzc2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d1arzd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d1arzd2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Dihydrodipicolinate reductase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GAPDH-like	8000961	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8000961	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8000961	3000043	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8000961	3000043	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	DapB_C	e1arzA1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
A	DapB_N	e1arzA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
B	DapB_C	e1arzB1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
B	DapB_N	e1arzB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
C	DapB_C	e1arzC1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
C	DapB_N	e1arzC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
D	DapB_C	e1arzD1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
D	DapB_N	e1arzD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05173	Dihydrodipicolinate reductase, C-terminus (DapB_C)	Dihydrodipicolinate reductase, C-terminus	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for bo ...	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.	Domain
A, B, C, D	PF01113	Dihydrodipicolinate reductase, N-terminus (DapB_N)	Dihydrodipicolinate reductase, N-terminus	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for b ...	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	DIHYDRODIPICOLINATE REDUCTASE	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity 4-hydroxy-tetrahydrodipicolinate reductase binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity 4-hydroxy-tetrahydrodipicolinate reductase oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor NAD binding identical protein binding protein binding	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process diaminopimelate biosynthetic process oxoacid metabolic process cellular biosynthetic process lipid biosynthetic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process diaminopimelate biosynthetic process oxoacid metabolic process cellular biosynthetic process lipid biosynthetic 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 fatty acid derivative metabolic process diaminopimelate 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000846	Dihydrodipicolinate reductase, N-terminal	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR022663	Dihydrodipicolinate reductase, C-terminal	Domain
A, B, C, D	IPR023940	Dihydrodipicolinate reductase	Family
A, B, C, D	IPR022664	Dihydrodipicolinate reductase, conserved site	Conserved Site

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	dihydrodipicolinate reductase M-CSA #402	Dihydrodipicolinate reductase catalyses the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. It can use both NADH and NADPH as a reductant, with NADH being twice as effective as NADPH The enzyme is a component of the biosynthetic pathway that leads to diaminopimelate and lysine in bacteria and higher plants. Because these pathways are unique to microorganisms and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds.	Defined by 2 residues: HIS:A-159LYS:A-163 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.3.1.26 (PDB Primary Data) Search M-CSA Motif + EC 1.3.1.26 EC: 1.17.1.8 (UniProt) Search M-CSA Motif + EC 1.17.1.8

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.