1I3J

CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
C [auth A]	d1i3ja_	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	DNA-binding domain of intron endonuclease I-TevI	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	DNA-binding domain of intron-encoded endonucleases	8021193	4003725	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	DNA-binding domain of intron-encoded endonucleases	8033573	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)
C [auth A]	GIY-YIG_Cterm	e1i3jA2	A: alpha arrays	X: HTH	H: HTH	T: DNA-binding domain of intron-encoded endonucleases	F: GIY-YIG_Cterm	ECOD (1.6)
C [auth A]	GIY-YIG_Cterm_like	e1i3jA3	A: few secondary structure elements	X: Zinc finger domain in intron-associated endonuclease 1 (From Topology)	H: Zinc finger domain in intron-associated endonuclease 1 (From Topology)	T: Zinc finger domain in intron-associated endonuclease 1	F: GIY-YIG_Cterm_like	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF20987	Intron-encoded endonuclease 1, DNA-binding domain (I-TevI_DNA-bd)	Intron-encoded endonuclease 1, DNA-binding domain	This domain is found in Intron-encoded endonuclease 1 (I-TevI) from Bacteriophage T4. I-TevI is a site-specific endonuclease that belongs to the GIY-YIG family that shows a catalytic domain (Pfam:PF01541) and a DNA-binding domain (this entry), which ...	This domain is found in Intron-encoded endonuclease 1 (I-TevI) from Bacteriophage T4. I-TevI is a site-specific endonuclease that belongs to the GIY-YIG family that shows a catalytic domain (Pfam:PF01541) and a DNA-binding domain (this entry), which is organised into three DNA recognition subdomains: a Zn finger, an elongated subdomain that includes a minor groove-binding alpha- helix and a helix-turn-helix subdomain [1].	Domain
C [auth A]	PF22635	Intron-associated endonuclease 1 zinc finger domain (I-TevI_ZnF)	Intron-associated endonuclease 1 zinc finger domain	This entry represent the unusual zinc finger domain present in the -ntron-associated endonuclease 1 (I-TevI) [1,2], which comprises the unusual sequence CXCX10CXXC. The Zn finger interacts with the DNA through two hydrogen bonds, between the main cha ...	This entry represent the unusual zinc finger domain present in the -ntron-associated endonuclease 1 (I-TevI) [1,2], which comprises the unusual sequence CXCX10CXXC. The Zn finger interacts with the DNA through two hydrogen bonds, between the main chain nitrogen atoms of residues Tyr162 and Ser165 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	5'-D(TPTPCPTPTPGPGPGPTPCPTPAPCPCPGPTPTPTPAPAP*T)-3'	-	-	-
B [auth C]	5'-D(APAPTPTPAPAPAPCPGPGPTPAPGPAPCPCPCPAPAPGP*A)-3'	-	-	-
C [auth A]	INTRON-ASSOCIATED ENDONUCLEASE 1	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding sequence-specific DNA binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process DNA recombination DNA metabolic process intron homing	protein-containing complex transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR006350	Intron endonuclease, group I	Family
C [auth A]	IPR048681	Intron-encoded endonuclease 1, DNA-binding domain	Domain
C [auth A]	IPR003611	Nuclease associated modular domain 3	Domain
C [auth A]	IPR035901	GIY-YIG endonuclease superfamily	Homologous Superfamily
C [auth A]	IPR000305	GIY-YIG endonuclease	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.