2FG0

Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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	d2fg0a1	All beta proteins	SH3-like barrel	Prokaryotic SH3-related domain	Spr N-terminal domain-like	Cell wall-associated hydrolase Spr N-terminal domain	(Nostoc punctiforme PCC 73102 ) [TaxId: 63737 ],	SCOPe (2.08)
A	d2fg0a2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	NlpC/P60	Cell wall-associated hydrolase Spr C-terminal domain	(Nostoc punctiforme PCC 73102 ) [TaxId: 63737 ],	SCOPe (2.08)
B	d2fg0b1	All beta proteins	SH3-like barrel	Prokaryotic SH3-related domain	Spr N-terminal domain-like	Cell wall-associated hydrolase Spr N-terminal domain	(Nostoc punctiforme PCC 73102 ) [TaxId: 63737 ],	SCOPe (2.08)
B	d2fg0b2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	NlpC/P60	Cell wall-associated hydrolase Spr C-terminal domain	(Nostoc punctiforme PCC 73102 ) [TaxId: 63737 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Prokaryotic SH3-related domain	8040216	3001455	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8040218	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8040218	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Prokaryotic SH3-related domain	8040216	3001455	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	SH3_3_2	e2fg0A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_3_2	ECOD (1.6)
A	NLPC_P60	e2fg0A2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: NLPC_P60	ECOD (1.6)
B	SH3_3_2	e2fg0B1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_3_2	ECOD (1.6)
B	NLPC_P60	e2fg0B2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: NLPC_P60	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
A	3.90.1720.10	Alpha Beta	Alpha-Beta Complex	endopeptidase fold (from Nostoc punctiforme)	endopeptidase domain like (from Nostoc punctiforme)	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	3.90.1720.10	Alpha Beta	Alpha-Beta Complex	endopeptidase fold (from Nostoc punctiforme)	endopeptidase domain like (from Nostoc punctiforme)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00877	NlpC/P60 family (NLPC_P60)	NlpC/P60 family	-	Family
A, B	PF18348	Bacterial dipeptidyl-peptidase Sh3 domain (SH3_16)	Bacterial dipeptidyl-peptidase Sh3 domain	This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by co ...	This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed [1].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000064	Endopeptidase, NLPC/P60 domain	Domain
A, B	IPR041382	Bacterial dipeptidyl-peptidase SH3 domain	Domain
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR051202	Peptidase C40	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 R01GM133198.