Annotations: 1TUF

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1tufb1	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	d1tufb2	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)
A	d1tufa1	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	d1tufa2	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)
B	SCOP2B Superfamily	PLP-binding barrel	8040495	3000273	SCOP2B (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)
A	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-binding barrel	8040495	3000273	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8040501	3001044	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)
B	Trypsin	e1tufB1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Trypsin	ECOD (v295.2)
B	NAD_binding_3	e1tufB2	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)
A	Trypsin	e1tufA1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Trypsin	ECOD (v295.2)
A	NAD_binding_3	e1tufA2	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: NAD_binding_3	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	Diaminopimelate decarboxylase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding diaminopimelate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	LLP	Parent Component: LYS : AA0119 : N6-pyridoxal phosphate-L-lysine MOD:00128