4PBA | pdb_00004pba

The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with Substrate-like DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family 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	EUF07529	e4pbaD2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: EUF07529	ECOD (1.6)
D	YcjD_like	e4pbaD1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YcjD_like	ECOD (1.6)
C	EUF07529	e4pbaC2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: EUF07529	ECOD (1.6)
C	YcjD_like	e4pbaC1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YcjD_like	ECOD (1.6)
B [auth A]	EUF07529	e4pbaA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: EUF07529	ECOD (1.6)
B [auth A]	YcjD_like	e4pbaA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YcjD_like	ECOD (1.6)
A [auth B]	EUF07529	e4pbaB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: EUF07529	ECOD (1.6)
A [auth B]	YcjD_like	e4pbaB1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YcjD_like	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C, D	PF21598	Restriction endonuclease PvuRts1 I-like, N-terminal (PvuRts1I-like_N)	Restriction endonuclease PvuRts1 I-like, N-terminal	This domain is found at the N-terminal end of Restriction endonuclease PvuRts1 I from Proteus vulgaris and similar bacterial sequences. PvuRts1I a modification-dependent endonuclease with high selectivity for 5-hydroxymethylcytosine, an epigenetic ma ...	This domain is found at the N-terminal end of Restriction endonuclease PvuRts1 I from Proteus vulgaris and similar bacterial sequences. PvuRts1I a modification-dependent endonuclease with high selectivity for 5-hydroxymethylcytosine, an epigenetic marker that is crucial for multiple biological processes, over 5-methylcytosine and cytosine. This protein is organised into a nuclease domain (this entry) and a C-terminal SRA domain (Pfam:PF18491). This domain adopts a typical three- layered alpha-beta-alpha sandwich configuration, with a central five-stranded beta-sheet surrounded by three alpha-helices on one side and one alpha-helix on the other side [1-3].	Domain
A [auth B], B [auth A], C, D	PF18491	SET and RING associated domain (SRA)	SET and RING associated domain	This is the C-terminal domain found in PvuRts1I, a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA in bacteria. Structural analys ...	This is the C-terminal domain found in PvuRts1I, a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA in bacteria. Structural analysis indicates that it has the typical SRA (SET and RING associated) domain fold (Pfam:PF02182) [1].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D	IPR040674	PvuRts1 I-like, SET and RING associated domain	Domain
A [auth B], B [auth A], C, D	IPR048797	Restriction endonuclease PvuRts1 I-like, N-terminal	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.