1TWI

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine

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	d1twia1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1twia2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1twib1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1twib2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1twic1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1twic2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1twid1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1twid2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Diaminopimelate decarboxylase LysA	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Alanine racemase-like, N-terminal domain	8028116	4003111	SCOP2 (2022-06-29)
A	SCOP2 Family	Eukaryotic ODC-like	8028122	4003520	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-binding barrel	8040495	3000273	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-binding barrel	8040495	3000273	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-binding barrel	8040495	3000273	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-binding barrel	8040495	3000273	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	Orn_DAP_Arg_deC_C	e1twiA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
A	Orn_DAP_Arg_deC_N	e1twiA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)
B	Orn_DAP_Arg_deC_C	e1twiB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
B	Orn_DAP_Arg_deC_N	e1twiB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)
C	Orn_DAP_Arg_deC_C	e1twiC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
C	Orn_DAP_Arg_deC_N	e1twiC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)
D	Orn_DAP_Arg_deC_C	e1twiD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
D	Orn_DAP_Arg_deC_N	e1twiD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
B	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
B	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
C	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
C	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
D	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
D	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain (Orn_Arg_deC_N)	Pyridoxal-dependent decarboxylase, pyridoxal binding domain	These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.	Domain
A, B, C, D	PF00278	Pyridoxal-dependent decarboxylase, C-terminal sheet domain (Orn_DAP_Arg_deC)	Pyridoxal-dependent decarboxylase, C-terminal sheet domain	These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Diaminopimelate decarboxylase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding diaminopimelate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process diaminopimelate metabolic process fatty acid derivative metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B, C, D	IPR022643	Orn/DAP/Arg decarboxylase 2, C-terminal	Domain
A, B, C, D	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B, C, D	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A, B, C, D	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site	Conserved Site
A, B, C, D	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	Domain
A, B, C, D	IPR002986	Diaminopimelate decarboxylase, LysA	Family
A, B, C, D	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site	Binding Site

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.