1U3E

DNA binding and cleavage by the HNH homing endonuclease I-HmuI

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
D [auth M]	d1u3em1	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Intron-encoded homing endonucleases	Intron-encoded homing endonuclease I-HmuI	(Okubovirus SPO1 ) [TaxId: 10685 ],	SCOPe (2.08)
D [auth M]	d1u3em2	Alpha and beta proteins (a+b)	DNA-binding domain of intron-encoded endonucleases	DNA-binding domain of intron-encoded endonucleases	DNA-binding domain of intron-encoded endonucleases	Intron-encoded homing endonuclease I-HmuI	(Okubovirus SPO1 ) [TaxId: 10685 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth M]	SCOP2 Family	Intron-encoded homing endonucleases	8028321	4000891	SCOP2 (2022-06-29)
D [auth M]	SCOP2 Family	DNA-binding domain of intron-encoded endonucleases	8028322	4003725	SCOP2 (2022-06-29)
D [auth M]	SCOP2 Superfamily	His-Me finger endonucleases	8040700	3001893	SCOP2 (2022-06-29)
D [auth M]	SCOP2 Superfamily	DNA-binding domain of intron-encoded endonucleases	8040701	3001361	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth M]	IENR1	e1u3eM1	A: alpha arrays	X: HTH	H: HTH	T: DNA-binding domain of intron-encoded endonucleases	F: IENR1	ECOD (1.6)
D [auth M]	HNH_3	e1u3eM2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth M]	3.90.75.20	Alpha Beta	Alpha-Beta Complex	Homing Intron 3 (I-Ppo) Encoded Endonuclease	Chain A	CATH (4.3.0)
D [auth M]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth M]	PF13392	HNH endonuclease (HNH_3)	HNH endonuclease	This is a zinc-binding loop of Fold group 7 [1] as found in endo-deoxy-ribonucleases and HNH nucleases.	Domain
D [auth M]	PF07463	NUMOD4 motif (NUMOD4)	NUMOD4 motif	-	Motif
D [auth M]	PF22083	DNA endonuclease I-HmuI-like, NUMOD-like domain (I-HmuI_NUMOD-like)	DNA endonuclease I-HmuI-like, NUMOD-like domain	This entry represents a C-terminal NUMOD1-like DNA-binding (HTH superfamily) domain present in a set of intron-encoded endonucleases (homing endonucleases) such as I-HmuI from Bacteriophage SP01 and similar proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	36-MER	-	-	-
B	5'-D(CPTPTPAPCPGPTPGPGPGPAPAPTPTPGPCPTPGPAPGP*C)-3'	-	-	-
C	5'-D(PGPTPTPAPGPGPCPTPCPAPTPTPAPCP*T)-3'	-	-	-
D [auth M]	HNH homing endonuclease	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity	nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process intron homing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth M]	IPR054307	DNA endonuclease I-HmuI-like, NUMOD-like domain	Domain
D [auth M]	IPR003647	Intron encoded nuclease repeat	Repeat
D [auth M]	IPR010902	NUMOD4	Domain
D [auth M]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
D [auth M]	IPR044925	His-Me finger superfamily	Homologous Superfamily
D [auth M]	IPR003615	HNH nuclease	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.