3UI3 | pdb_00003ui3

Structural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8090290	3000399	SCOP2B (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	CRISPR_Cas2	e3ui3B1	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR associated protein Cas2-like (From Topology)	T: CRISPR associated protein Cas2-like	F: CRISPR_Cas2	ECOD (1.6)
A	IgG_binding_B	e3ui3A5	A: a+b two layers	X: beta-Grasp	H: Immunoglobulin-binding domains (From Topology)	T: Immunoglobulin-binding domains	F: IgG_binding_B	ECOD (1.6)
A	CRISPR_Cas2	e3ui3A6	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR associated protein Cas2-like (From Topology)	T: CRISPR associated protein Cas2-like	F: CRISPR_Cas2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09827	CRISPR associated protein Cas2 (CRISPR_Cas2)	CRISPR associated protein Cas2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Immunoglobulin G-binding protein G, Virulence-associated protein D	hydrolase activity catalytic activity nuclease activity catalytic activity, acting on a nucleic acid RNA binding binding nucleic acid binding protein-containing complex binding immunoglobulin binding IgG binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019199	Virulence-associated protein D / CRISPR associated protein Cas2	Family
A, B	IPR016368	Endoribonuclease VapD	Family
A, B	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
A, B	IPR005877	YSIRK Gram-positive signal peptide	Domain
A, B	IPR000724	IgG-binding B	Domain
A, B	IPR019950	M protein-type anchor motif	Conserved Site
A, B	IPR035152	GA-like domain	Domain
A, B	IPR019931	LPXTG cell wall anchor motif	Conserved Site

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.