2IQ7 | pdb_00002iq7

Crystal structure of the polygalacturonase from Colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G	d2iq7g_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)
F	d2iq7f_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)
E	d2iq7e_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)
D	d2iq7d_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)
C	d2iq7c_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)
B	d2iq7b_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)
A	d2iq7a_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Galacturonase	automated matches	(Colletotrichum lupini ) [TaxId: 145971 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Pectin lyase-like	8067059	3001746	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Pectin lyase-like	8067059	3001746	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Pectin lyase-like	8067059	3001746	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pectin lyase-like	8067059	3001746	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pectin lyase-like	8067059	3001746	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pectin lyase-like	8067059	3001746	SCOP2B (2022-06-29)
A	SCOP2 Family	Galacturonase	8067058	4002799	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pectin lyase-like	8067059	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)
G	Rpf1_C	e2iq7G1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
F	Rpf1_C	e2iq7F1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
E	Rpf1_C	e2iq7E1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
D	Rpf1_C	e2iq7D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
C	Rpf1_C	e2iq7C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
B	Rpf1_C	e2iq7B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (v294.1)
A	TGF_beta	e2iq7A1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: TGF_beta	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	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)
F	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)
E	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)
D	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)
C	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)
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, C, D, E A, B, C, D, E, F, G	endopolygalacturonase	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity polygalacturonase activity catalytic 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, C, D, E A, B, C, D, E, F, G	IPR006626	Parallel beta-helix repeat	Repeat
A, B, C, D, E A, B, C, D, E, F, G	IPR012334	Pectin lyase fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR050434	Glycosyl hydrolase family 28, fungi	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR000743	Glycoside hydrolase, family 28	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily

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.