5HR4

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering of new specificities

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 [auth C]	PF20465	e5hr4C3	A: alpha arrays	X: N-terminal helical domain in restriction-modification system methylation subunit-like	H: N-terminal helical domain in restriction-modification system methylation subunit (From Topology)	T: N-terminal helical domain in restriction-modification system methylation subunit	F: PF20465	ECOD (1.6)
A [auth C]	PF20466,PF20467	e5hr4C1	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: PF20466,PF20467	ECOD (1.6)
A [auth C]	PF20473	e5hr4C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF20473	ECOD (1.6)
D [auth J]	PF20465	e5hr4J1	A: alpha arrays	X: N-terminal helical domain in restriction-modification system methylation subunit-like	H: N-terminal helical domain in restriction-modification system methylation subunit (From Topology)	T: N-terminal helical domain in restriction-modification system methylation subunit	F: PF20465	ECOD (1.6)
D [auth J]	PF20466,PF20467	e5hr4J3	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: PF20466,PF20467	ECOD (1.6)
D [auth J]	PF20473	e5hr4J2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF20473	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], D [auth J]	PF20473	MmeI, DNA-methyltransferase domain (MmeI_Mtase)	MmeI, DNA-methyltransferase domain	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease doma ...	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove [1]. This domain corresponds to the DNA-methyltransferase. Structurally, it consists of a twisted beta-sheet flanked by alpha-helices on both sides.	Domain
A [auth C], D [auth J]	PF20464	MmeI, N-terminal domain (MmeI_N)	MmeI, N-terminal domain	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease doma ...	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. This domain corresponds to the N-terminal endonuclease, it cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage [2].	Domain
A [auth C], D [auth J]	PF20465	MmeI, helicase spacer domain (MmeI_hel)	MmeI, helicase spacer domain	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease doma ...	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The endonuclease cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage [2]. This domain corresponds to the multi-helical spacer. It is thought to play a key role in positioning the endonuclease cleavage domain correctly.	Domain
A [auth C], D [auth J]	PF20466	MmeI, target recognition domain (MmeI_TRD)	MmeI, target recognition domain	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease doma ...	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove [1]. This domain corresponds to the TRD. It consists of two alpha/beta subdomains.	Domain
A [auth C], D [auth J]	PF20467	MmeI, C-terminal domain (MmeI_C)	MmeI, C-terminal domain	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease doma ...	Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove [1]. This domain corresponds to the C-terminal region.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], D [auth J]	MmeI	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	methylation metabolic process	-
B [auth H], E [auth K]	DNA (5'-D(PTPAPTPCPCPGPAPCPAPTPAPAP*C)-3')	-	-	-
C [auth I], F [auth L]	DNA (5'-D(PGPTPTPAPTPGPTPCPGPGPAPTP*A)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], D [auth J]	IPR046816	MmeI-like, DNA-methyltransferase domain	Domain
A [auth C], D [auth J]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth C], D [auth J]	IPR046820	MmeI-like, target recognition domain	Domain
A [auth C], D [auth J]	IPR046818	MmeI-like, C-terminal domain	Domain
A [auth C], D [auth J]	IPR046819	MmeI-like, helicase spacer domain	Domain
A [auth C], D [auth J]	IPR046817	MmeI-like, N-terminal domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.