Annotations: 6SEI

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	PF01541	e6seiC1	A: a+b three layers	X: GIY-YIG endonuclease (From Topology)	H: GIY-YIG endonuclease (From Topology)	T: GIY-YIG endonuclease	F: PF01541	ECOD (1.6)
C	PF21202	e6seiC2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF21202	ECOD (1.6)
A	PF01541	e6seiA1	A: a+b three layers	X: GIY-YIG endonuclease (From Topology)	H: GIY-YIG endonuclease (From Topology)	T: GIY-YIG endonuclease	F: PF01541	ECOD (1.6)
A	PF21202	e6seiA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF21202	ECOD (1.6)
D	PF09494	e6seiD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF09494	ECOD (1.6)
B	PF09494	e6seiB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF09494	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, C	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
B, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Structure-specific endonuclease subunit SLX1	5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity DNA endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA flap endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle Slx1-Slx4 complex nuclear lumen non-membrane-bounded organelle
B, D	Structure-specific endonuclease subunit SLX4	DNA binding binding organic cyclic compound binding nucleic acid binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity DNA endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA binding binding organic cyclic compound binding nucleic acid binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity DNA endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA flap endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription regulation of metabolic process cellular component organization organelle organization cellular component organization or biogenesis 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 chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle Slx1-Slx4 complex nuclear lumen non-membrane-bounded organelle
E	DNA (32-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR027520	Structure-specific endonuclease subunit Slx1	Family
A, C	IPR035901	GIY-YIG endonuclease superfamily	Homologous Superfamily
A, C	IPR000305	GIY-YIG endonuclease	Domain
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR048749	Structure-specific endonuclease subunit SLX1, C-terminal domain	Domain
B, D	IPR017956	AT hook, DNA-binding motif	Conserved Site
B, D	IPR027784	Structure-specific endonuclease subunit Slx4, ascomycetes	Family
B, D	IPR000637	HMG-I/HMG-Y, DNA-binding, conserved site	Conserved Site
B, D	IPR018574	Structure-specific endonuclease subunit Slx4	Family

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 R01GM133198.