2IBT | pdb_00002ibt

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth D]	d2ibtd1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	DNA methylase TaqI, N-terminal domain	DNA methylase TaqI, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
F [auth D]	d2ibtd2	Alpha and beta proteins (a+b)	DNA methylase specificity domain	DNA methylase specificity domain	TaqI C-terminal domain-like	DNA methylase TaqI, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E [auth A]	d2ibta1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	DNA methylase TaqI, N-terminal domain	DNA methylase TaqI, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E [auth A]	d2ibta2	Alpha and beta proteins (a+b)	DNA methylase specificity domain	DNA methylase specificity domain	TaqI C-terminal domain-like	DNA methylase TaqI, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth D]	SCOP2B Superfamily	DNA methylase specificity domain	8034513	3001742	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8034512	3000118	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	DNA methylase specificity domain	8034513	3001742	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8034512	3000118	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)
F [auth D]		e2ibtD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
F [auth D]		e2ibtD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CMAS, Methyltransf_25	F:	ECOD (20:10:01)
E [auth A]		e2ibtA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
E [auth A]		e2ibtA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CMAS, Methyltransf_25	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth D]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
F [auth D]	3.90.220.10	Alpha Beta	Alpha-Beta Complex	Adenine-n6-DNA-methyltransferase TaqI	Chain A, domain 2	CATH (4.3.0)
E [auth A]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
E [auth A]	3.90.220.10	Alpha Beta	Alpha-Beta Complex	Adenine-n6-DNA-methyltransferase TaqI	Chain A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth D]	Modification methylase TaqI	DNA binding binding nucleic acid binding DNA-methyltransferase activity catalytic activity, acting on DNA site-specific DNA-methyltransferase (adenine-specific) activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity	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	-
B [auth C], D [auth F]	5'-D(GPAPCPAP(3DR)PCPGP(6MA)PAPC)-3'	-	-	-
A [auth B], C [auth E]	5'-D(GPTPTPCPGP(2PR)PTPGPTPC)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth D]	IPR050953	N(4)/N(6)-adenine-specific DNA methyltransferase	Family
E [auth A], F [auth D]	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
E [auth A], F [auth D]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
E [auth A], F [auth D]	IPR025931	TaqI-like C-terminal specificity domain	Domain
E [auth A], F [auth D]	IPR021188	N6 adenine-specific DNA methyltransferase, TaqI class	Family
E [auth A], F [auth D]	IPR023135	N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal	Homologous Superfamily
E [auth A], F [auth D]	IPR011639	Type II methyltransferase M.TaqI-like domain	Domain

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.