4Q2D

Crystal Structure of CRISPR-Associated protein in complex with 2'-Deoxyadenosine 5'-Triphosphate

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)
A	PF18019	e4q2dA3	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
A	PF18395	e4q2dA4	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 C-terminal domain (From Topology)	T: Cas3 C-terminal domain	F: PF18395	ECOD (1.6)
A	F_UNCLASSIFIED	e4q2dA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF22590	e4q2dA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3210.30	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18395	Cas3 C-terminal domain (Cas3_C)	Cas3 C-terminal domain	This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal ...	This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal HD nuclease activity by functioning as a substrate filter [1].	Domain
A	PF18019	Cas3, HD domain (Cas3_HD)	Cas3, HD domain	This HD domain is found at the N-terminus of Cas3 enzymes fused to a helicase domain. This domain is sometimes found as a separate protein. It acts as a nuclease that cleaves ssDNA.	Domain
A	PF22590	CRISPR-associated nuclease/helicase Cas3, C-terminal (Cas3-like_C_2)	CRISPR-associated nuclease/helicase Cas3, C-terminal	This entry represents the C-terminal domain of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa (Cas3), a DNA-degradation enzyme that forms part of the CRISPR-Cas bacterial immune system. Cas3 contains a Cas2 dom ...	This entry represents the C-terminal domain of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa (Cas3), a DNA-degradation enzyme that forms part of the CRISPR-Cas bacterial immune system. Cas3 contains a Cas2 domain, an HD nuclease domain (Pfam:PF18019), RecA1, RecA2, a long linker region, and a C-terminal domain (this entry). This domain contains two alpha-helices and two six-stranded beta-blades [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CRISPR-associated helicase Cas3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity cation binding metal ion binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR038257	CRISPR-associated Cas3-type HD domain superfamily	Homologous Superfamily
A	IPR006474	Helicase Cas3, CRISPR-associated, core	Domain
A	IPR041372	Cas3, C-terminal	Domain
A	IPR006483	CRISPR-associated Cas3-type, HD domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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 R01GM133198.