2C1G

Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA)

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	d2c1ga1	Alpha and beta proteins (a/b)	7-stranded beta/alpha barrel	Glycoside hydrolase/deacetylase	NodB-like polysaccharide deacetylase	Peptidoglycan GlcNAc deacetylase C-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d2c1ga2	Alpha and beta proteins (a+b)	Peptidoglycan deacetylase N-terminal noncatalytic region	Peptidoglycan deacetylase N-terminal noncatalytic region	Peptidoglycan deacetylase N-terminal noncatalytic region	Peptidoglycan GlcNAc deacetylase	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	NodB-like	8026698	4000448	SCOP2 (2022-06-29)
A	SCOP2 Family	Peptidoglycan deacetylase N-terminal noncatalytic region	8026700	4000425	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glycoside hydrolase/deacetylase	8039077	3001025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Peptidoglycan deacetylase N-terminal noncatalytic region	8039079	3000265	SCOP2 (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	EUF08442	e2c1gA1	A: a+b two layers	X: Peptidoglycan deacetylase N-terminal noncatalytic region (From Topology)	H: Peptidoglycan deacetylase N-terminal noncatalytic region (From Topology)	T: Peptidoglycan deacetylase N-terminal noncatalytic region	F: EUF08442	ECOD (1.6)
A	Polysacc_deac_1	e2c1gA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase (From Topology)	T: Glycoside hydrolase/deacetylase	F: Polysacc_deac_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.565.50	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90		CATH (4.3.0)
A	3.90.640.30	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
A	3.20.20.370	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase/deacetylase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18627	Peptidoglycan GlcNAc deacetylase N-terminal domain (PgdA_N)	Peptidoglycan GlcNAc deacetylase N-terminal domain	This is the N-terminal and middle domain found in Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA). PgdA protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. It is a memb ...	This is the N-terminal and middle domain found in Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA). PgdA protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. It is a member of the family 4 carbohydrate esterases (CE-4) [1].	Domain
A	PF01522	Polysaccharide deacetylase (Polysacc_deac_1)	Polysaccharide deacetylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PEPTIDOGLYCAN GLCNAC DEACETYLASE	enzyme regulator activity molecular function inhibitor activity lysozyme inhibitor activity molecular function regulator activity enzyme inhibitor activity deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity N-acetylglucosamine deacetylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding enzyme regulator activity molecular function inhibitor activity lysozyme inhibitor activity molecular function regulator activity enzyme inhibitor activity deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity N-acetylglucosamine deacetylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular component organization cell wall modification cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization carbohydrate metabolic process primary metabolic process metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011330	Glycoside hydrolase/deacetylase, beta/alpha-barrel	Homologous Superfamily
A	IPR054897	N-acetylglucosamine deacetylase	Family
A	IPR017219	Peptidoglycan GlcNAc deacetylase	Family
A	IPR050248	Polysaccharide deacetylase, ArnD subfamily	Family
A	IPR002509	NodB homology domain	Domain
A	IPR040802	Peptidoglycan GlcNAc deacetylase, N-terminal	Domain

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.