2Z8R | pdb_00002z8r

Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	CBM_5_12	e2z8rB2	A: alpha bundles	X: C-terminal domain in some PLP-dependent transferases	H: C-terminal domain in some PLP-dependent transferases	T: C-terminal domain in some PLP-dependent transferases	F: CBM_5_12	ECOD (develop294)
B	WD40	e2z8rB3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: WD40	ECOD (develop294)
A		e2z8rA1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18370	Rhamnogalacturonan I lyases beta-sheet domain (RGI_lyase)	Rhamnogalacturonan I lyases beta-sheet domain	This is the beta-sheet domain found in rhamnogalacturonan (RG) lyases [1], which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 carrying this domain, such as YesW (EC:4 ...	This is the beta-sheet domain found in rhamnogalacturonan (RG) lyases [1], which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 carrying this domain, such as YesW (EC:4.2.2.23) and YesX (EC:4.2.2.24), cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction [2]. Other family members carrying this domain are hemagglutinin A, lysine gingipain (Kgp) [3] and Chitinase C (EC:3.2.1.14).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	YesW protein	cation binding ion binding binding metal ion binding small molecule binding rhamnogalacturonan endolyase activity lyase activity carbon-oxygen lyase activity, acting on polysaccharides catalytic activity carbon-oxygen lyase activity	cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
A, B	IPR041624	Rhamnogalacturonan I lyase beta-sheet domain	Domain
A, B	IPR034641	Polysaccharide lyase family 11	Family
A, B	IPR049366	Rhamnogalacturonan lyase family 11, C-terminal domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.