1RU4

Crystal structure of pectate lyase Pel9A

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
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)
A	d1ru4a_	All beta proteins	Single-stranded right-handed beta-helix	Pectin lyase-like	Pectate transeliminase	Pectate transeliminase	(Dickeya chrysanthemi ) [TaxId: 556 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pectate transeliminase	8028546	4000952	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pectin lyase-like	8040925	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)
A	DUF4990	e1ru4A1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pectin lyase-like (From Topology)	T: Pectin lyase-like	F: DUF4990	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13229	Right handed beta helix region (Beta_helix)	Right handed beta helix region	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Pectate lyase	cation binding ion binding binding metal ion binding small molecule binding pectate lyase activity lyase activity carbon-oxygen lyase activity, acting on polysaccharides catalytic activity carbon-oxygen lyase activity	symbiont-mediated disruption of host anatomical structure disruption of cellular anatomical structure in another organism biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cellular anatomical entity disruption of cell wall in another organism symbiont-mediated disruption of host cell wall disruption of anatomical structure in another organism symbiont-mediated disruption of host cell envelope carbohydrate metabolic process galacturonan metabolic process catabolic process pectin metabolic process carbohydrate catabolic process primary metabolic process symbiont-mediated disruption of host anatomical structure disruption of cellular anatomical structure in another organism biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cellular anatomical entity disruption of cell wall in another organism symbiont-mediated disruption of host cell wall disruption of anatomical structure in another organism symbiont-mediated disruption of host cell envelope carbohydrate metabolic process galacturonan 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	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006626	Parallel beta-helix repeat	Repeat
A	IPR012334	Pectin lyase fold	Homologous Superfamily
A	IPR052052	Polysaccharide Lyase 9	Family
A	IPR053868	Pel9A-like, right handed beta-helix region	Domain
A	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	pectate lyase L (polysaccharide lyase 9 family) M-CSA #184	Endo-acting pectate lyase L (Pel9A) is from the bacteria Erwini chrysanthemi. It catalyses the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends. This particular bacteria causes soft rot diseases. It secretes enzymes such as Pel9A which break down pectin, a key component of cell walls.	Defined by 2 residues: ASN:A-243 [auth A-268]LYS:A-248 [auth A-273] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2.2.2 (PDB Primary Data) Search M-CSA Motif + EC 4.2.2.2

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.