5FFJ | pdb_00005ffj

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
Domain Annotation: CATH
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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	DNA (5'-D(PTPAPGPCPTPAPAPTPAPGPAPCPTPGPGPAPTPGPGPAPGPG)-3')	-	-	-
B [auth D], E	DNA (5'-D(PTPCPCPTPCPCPAPTPCPCPAPGPTPCPTPAPTPTPAPGPCPT)-3')	-	-	-
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 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 endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid	methylation metabolic process cellular process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process methylation metabolic process cellular process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification defense response to other organism response to stress macromolecule modification response to external biotic stimulus macromolecule metabolic process cellular response to stimulus SOS response cellular response to stress DNA damage response	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	IPR050742	Helicase_Restrict-Modif_Enz	Unknown
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.