4XQK | pdb_00004xqk

ATP-dependent Type ISP restriction-modification enzyme LlaBIII bound to DNA

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	COG4889_1st	e4xqkB6	A: alpha arrays	X: N-terminal helical domain in restriction-modification system methylation subunit-like	H: Helical domain in type ISP restriction-modification enzymes (From Topology)	T: Helical domain in type ISP restriction-modification enzymes	F: COG4889_1st	ECOD (1.6)
B	COG4889_2nd	e4xqkB1	A: a+b complex topology	X: DNA methylase specificity domain (From Topology)	H: DNA methylase specificity domain (From Topology)	T: DNA methylase specificity domain	F: COG4889_2nd	ECOD (1.6)
B	N6_Mtase	e4xqkB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (1.6)
B	DEAD_1	e4xqkB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
B	Helicase_C_1	e4xqkB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
B	Mrr_cat_2	e4xqkB5	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Mrr_cat_2	ECOD (1.6)
A	COG4889_1st	e4xqkA5	A: alpha arrays	X: N-terminal helical domain in restriction-modification system methylation subunit-like	H: Helical domain in type ISP restriction-modification enzymes (From Topology)	T: Helical domain in type ISP restriction-modification enzymes	F: COG4889_1st	ECOD (1.6)
A	COG4889_2nd	e4xqkA6	A: a+b complex topology	X: DNA methylase specificity domain (From Topology)	H: DNA methylase specificity domain (From Topology)	T: DNA methylase specificity domain	F: COG4889_2nd	ECOD (1.6)
A	N6_Mtase	e4xqkA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (1.6)
A	DEAD_1	e4xqkA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
A	Helicase_C_1	e4xqkA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
A	Mrr_cat_2	e4xqkA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Mrr_cat_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18135	Type ISP C-terminal specificity domain (Type_ISP_C)	Type ISP C-terminal specificity domain	This is the C-terminal domain of Type ISP restriction-modification enzyme LLaBIII present in Lactococcus lactis subsp. cremoris. Type ISP restriction-modification (RM) enzymes provide a potent defence against infection by foreign and bacteriophage DN ...	This is the C-terminal domain of Type ISP restriction-modification enzyme LLaBIII present in Lactococcus lactis subsp. cremoris. Type ISP restriction-modification (RM) enzymes provide a potent defence against infection by foreign and bacteriophage DNA. This domain interacts extensively with DNA and is known as the target recognition domain (TRD). TRD works by recognising 6/7 base pairs of asymmetric sequence [1].	Domain
A, B	PF22240	Type ISP restriction-modification enzyme, coupler domain (ISP_coupler)	Type ISP restriction-modification enzyme, coupler domain	Type ISP restriction-modification (RM) enzymes cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. This entry represents the all-helical coupler domain of type ISP RM enzymes, which l ...	Type ISP restriction-modification (RM) enzymes cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. This entry represents the all-helical coupler domain of type ISP RM enzymes, which links the ATPase to the MTase and the C-terminal TRD (target recognition domain) domains and seems to play a key role in transferring conformational strain during initiation [1-3].	Domain
A, B	PF02384	N-6 DNA Methylase (N6_Mtase)	N-6 DNA Methylase	-	Family
A, B	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A, B	PF04851	Type III restriction enzyme, res subunit (ResIII)	Type III restriction enzyme, res subunit	-	Family
A, B	PF13156	Restriction endonuclease (Mrr_cat_2)	Restriction endonuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F	DNA (28-MER)	-	-	-
C, E	DNA (28-MER)	-	-	-
A, B	LlaBIII	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding transferase activity, transferring one-carbon groups N-methyltransferase activity transferase activity methyltransferase activity catalytic activity hydrolase activity	cellular response to stimulus SOS response cellular response to stress response to stimulus DNA damage response response to stress cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050742	Helicase and Restriction-Modification Enzyme	Family
A, B	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B	IPR003356	DNA methylase, adenine-specific	Domain
A, B	IPR006935	Helicase/UvrB, N-terminal	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR053980	Type ISP restriction-modification enzyme, coupler domain	Domain
A, B	IPR039442	Mrr-like domain	Domain
A, B	IPR041635	Type ISP restriction-modification enzyme LLaBIII, C-terminal specificity domain	Domain
A, B	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 R01GM157729.