6SEH | pdb_00006seh

Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease

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)
D [auth B]	Slx4	e6sehB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Slx4	ECOD (1.6)
B [auth D]	Slx4	e6sehD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Slx4	ECOD (1.6)
C [auth A]	GIY-YIG	e6sehA2	A: a+b three layers	X: GIY-YIG endonuclease (From Topology)	H: GIY-YIG endonuclease (From Topology)	T: GIY-YIG endonuclease	F: GIY-YIG	ECOD (1.6)
C [auth A]	KOG3005	e6sehA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: KOG3005	ECOD (1.6)
A [auth C]	GIY-YIG	e6sehC2	A: a+b three layers	X: GIY-YIG endonuclease (From Topology)	H: GIY-YIG endonuclease (From Topology)	T: GIY-YIG endonuclease	F: GIY-YIG	ECOD (1.6)
A [auth C]	KOG3005	e6sehC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: KOG3005	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth B]	PF09494	Slx4 endonuclease (Slx4)	Slx4 endonuclease	The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearin ...	The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [1].	Domain
A [auth C], C [auth A]	PF21202	Structure-specific endonuclease subunit SLX1, C-terminal (SLX1_C)	Structure-specific endonuclease subunit SLX1, C-terminal	Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand ...	Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA [1-3]. This is the RING zinc finger domain.	Domain
A [auth C], C [auth A]	PF01541	GIY-YIG catalytic domain (GIY-YIG)	GIY-YIG catalytic domain	This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and ...	This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices [4]. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D], D [auth B]	Structure-specific endonuclease subunit SLX4	5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA recombination	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle Slx1-Slx4 complex nuclear lumen
A [auth C], C [auth A]	Structure-specific endonuclease subunit SLX1	endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity cation binding ion binding binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding 5'-flap endonuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle Slx1-Slx4 complex nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth B]	IPR027784	Structure-specific endonuclease subunit Slx4, ascomycetes	Family
B [auth D], D [auth B]	IPR000637	HMG-I/HMG-Y, DNA-binding, conserved site	Conserved Site
B [auth D], D [auth B]	IPR018574	Structure-specific endonuclease subunit Slx4	Family
A [auth C], C [auth A]	IPR027520	Structure-specific endonuclease subunit Slx1	Family
A [auth C], C [auth A]	IPR050381	SLX1 structure-specific endonuclease	Family
A [auth C], C [auth A]	IPR035901	GIY-YIG endonuclease superfamily	Homologous Superfamily
A [auth C], C [auth A]	IPR000305	GIY-YIG endonuclease	Domain
A [auth C], C [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth C], C [auth A]	IPR048749	Structure-specific endonuclease subunit SLX1, C-terminal 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.