5FFJ

Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic

External Resource: Annotation

Domain Annotation: ECOD Classification
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	COG4889_1st	e5ffjA4	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	e5ffjA3	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	e5ffjA2	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	e5ffjA1	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)
D [auth B]	COG4889_1st	e5ffjB5	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)
D [auth B]	COG4889_2nd	e5ffjB4	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)
D [auth B]	N6_Mtase	e5ffjB3	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)
D [auth B]	DEAD_1	e5ffjB1	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)
D [auth B]	Helicase_C_1	e5ffjB2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth 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, D [auth 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, D [auth B]	PF02384	N-6 DNA Methylase (N6_Mtase)	N-6 DNA Methylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B]	Endonuclease and methylase LlaGI	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 DNA binding nucleic acid binding transferase activity, transferring one-carbon groups N-methyltransferase activity transferase activity methyltransferase activity catalytic activity DNA-methyltransferase activity catalytic activity, acting on DNA site-specific DNA-methyltransferase (adenine-specific) activity catalytic activity, acting on a nucleic acid S-adenosylmethionine-dependent methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity	methylation metabolic process	-
B [auth D], E	DNA (5'-D(PTPCPCPTPCPCPAPTPCPCPAPGPTPCPTPAPTPTPAPGPCPT)-3')	-	-	-
C, F	DNA (5'-D(PTPAPGPCPTPAPAPTPAPGPAPCPTPGPGPAPTPGPGPAPGPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR050742	Helicase and Restriction-Modification Enzyme	Family
A, D [auth B]	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A, D [auth B]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, D [auth B]	IPR003356	DNA methylase, adenine-specific	Domain
A, D [auth B]	IPR006935	Helicase/UvrB, N-terminal	Domain
A, D [auth B]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, D [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
A, D [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, D [auth B]	IPR053980	Type ISP restriction-modification enzyme, coupler domain	Domain
A, D [auth B]	IPR039442	Mrr-like domain	Domain
A, D [auth B]	IPR041635	Type ISP restriction-modification enzyme LLaBIII, C-terminal specificity domain	Domain
A, D [auth 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.