1CZF | pdb_00001czf

ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d1czfb_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	Polygalacturonase	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
A	d1czfa_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	Polygalacturonase	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Pectin lyase-like	8042980	3001746	SCOP2B (2022-06-29)
A	SCOP2 Family	Galacturonase	8030601	4002799	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pectin lyase-like	8042980	3001746	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)
B	Hexapep,Acetyltransf_11	e1czfB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
A	Hexapep,Acetyltransf_11	e1czfA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.160.20.10	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Single-stranded right-handed beta-helix, Pectin lyase-like	CATH (4.3.0)
A	2.160.20.10	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Single-stranded right-handed beta-helix, Pectin lyase-like	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	POLYGALACTURONASE II	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity polygalacturonase activity catalytic activity galacturan 1,4-alpha-galacturonidase activity	cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization carbohydrate metabolic process catabolic process pectin metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process pectin catabolic process polysaccharide metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization carbohydrate metabolic process catabolic process pectin metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process pectin catabolic process polysaccharide metabolic process polysaccharide catabolic process metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006626	Parallel beta-helix repeat	Repeat
A, B	IPR012334	Pectin lyase fold	Homologous Superfamily
A, B	IPR050434	Glycosyl hydrolase family 28, fungi	Family
A, B	IPR000743	Glycoside hydrolase, family 28	Family
A, B	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	polygalacturonase M-CSA #480	Polygalacturonases hydrolyse the 1,4 linkage of de-esterified pectase. The enzyme belongs to the family 28 of glycosyl hydrolases, catalysing hydrolysis with inversion of stereochemistry at the anomeric carbon	Defined by 6 residues: ASP:A-180ASP:A-201ASP:A-202HIS:A-223ARG:A-256LYS:A-258 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2.1.15 (PDB Primary Data) Search M-CSA Motif + EC 3.2.1.15

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.