1LWS

Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1lwsa1	All beta proteins	Hedgehog/intein (Hint) domain	Hedgehog/intein (Hint) domain	Intein (protein splicing domain)	VMA1-derived endonuclease (VDE) PI-Scei intein	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth A]	d1lwsa2	Alpha and beta proteins (a+b)	Homing endonuclease-like	Homing endonucleases	Intein endonuclease	VMA1-derived endonuclease (VDE) PI-SceI	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Hedgehog/intein (Hint) domain	8042232	3001979	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Homing endonucleases	8035774	3000266	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Homing endonucleases	8035772	3000266	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Hedgehog/intein (Hint) domain	8042232	3001979	SCOP2B (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]	Hom_end_hint_1st	e1lwsA1	A: beta complex topology	X: Hedgehog/intein (From Homology)	H: Hedgehog/intein	T: Hint	F: Hom_end_hint_1st	ECOD (1.6)
C [auth A]	Hom_end	e1lwsA3	A: a+b two layers	X: Homing endonucleases-like	H: Homing endonucleases (From Topology)	T: Homing endonucleases	F: Hom_end	ECOD (1.6)
C [auth A]	Hom_end_hint_2nd	e1lwsA2	A: a+b two layers	X: Homing endonucleases-like	H: Homing endonucleases (From Topology)	T: Homing endonucleases	F: Hom_end_hint_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	2.170.16.10	Mainly Beta	Beta Complex	Endonuclease - Pi-scei	Chain A, domain 1	CATH (4.3.0)
C [auth A]	3.10.28.10	Alpha Beta	Roll	Endonuclease I-creI	Homing endonucleases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)	ATP synthase alpha/beta family, nucleotide-binding domain	This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.	Domain
C [auth A]	PF05204	Homing endonuclease (Hom_end)	Homing endonuclease	Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life.	Domain
C [auth A]	PF05203	Hom_end-associated Hint (Hom_end_hint)	Hom_end-associated Hint	Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [1] revealed two domains: an endonucleolytic centre resembling the C-termina ...	Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [1] revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	PI-SceI DNA recognition region top strand	-	-	-
B [auth C]	PI-SceI DNA recognition region bottom strand	-	-	-
C [auth A]	ENDONUCLEASE PI-SCEI	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic ion channel activity proton channel activity proton-transporting ATP synthase activity, rotational mechanism monoatomic cation channel activity passive transmembrane transporter activity channel activity catalytic activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding RNA binding mRNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity	transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport nucleobase-containing compound metabolic process organic cyclic compound metabolic process transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process intron homing homeostatic process biological regulation intracellular pH reduction regulation of intracellular pH vesicle organization cellular component organization organelle organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis endosome organization intracellular chemical homeostasis cellular component organization or biogenesis regulation of biological quality endosomal lumen acidification monoatomic cation homeostasis endomembrane system organization regulation of cellular pH intracellular monoatomic ion homeostasis intein-mediated protein splicing organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis organic substance biosynthetic process protein processing protein metabolic process protein splicing Golgi lumen acidification vacuolar acidification	vacuolar membrane membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure catalytic complex membrane membrane protein complex proton-transporting V-type ATPase complex vacuole proton-transporting V-type ATPase, V1 domain cellular anatomical entity intracellular membrane-bounded organelle vacuolar proton-transporting V-type ATPase, V1 domain vacuolar membrane membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure catalytic complex membrane membrane protein complex proton-transporting V-type ATPase complex vacuole proton-transporting V-type ATPase, V1 domain cellular anatomical entity intracellular membrane-bounded organelle vacuolar proton-transporting V-type ATPase, V1 domain vacuolar proton-transporting V-type ATPase complex intracellular organelle bounding membrane of organelle proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain organelle cytoplasm organelle membrane storage vacuole lytic vacuole fungal-type vacuole lytic vacuole membrane fungal-type vacuole membrane Golgi membrane Golgi apparatus endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR036844	Hint domain superfamily	Homologous Superfamily
C [auth A]	IPR022878	V-type ATP synthase catalytic alpha chain	Family
C [auth A]	IPR006142	Intein	Domain
C [auth A]	IPR007868	Hom-end-associated Hint	Domain
C [auth A]	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal	Homologous Superfamily
C [auth A]	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Homologous Superfamily
C [auth A]	IPR006141	Intein N-terminal splicing region	PTM
C [auth A]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
C [auth A]	IPR003586	Hint domain C-terminal	Domain
C [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth A]	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
C [auth A]	IPR031686	ATPsynthase alpha/beta subunit, N-terminal extension	Domain
C [auth A]	IPR004042	Intein DOD homing endonuclease	Domain
C [auth A]	IPR027434	Homing endonuclease	Homologous Superfamily
C [auth A]	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
C [auth A]	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
C [auth A]	IPR003587	Hint domain N-terminal	Domain
C [auth A]	IPR030934	Intein C-terminal splicing region	Domain
C [auth A]	IPR007869	Homing endonuclease PI-Sce	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
C [auth A]	H+-transporting two-sector ATPase (V-type) M-CSA #508	The homing endonuclease from S. cerevisiae, PI-SceI is able to catalyse the specific cleavage of double stranded DNA in order to allow the incorporation of a mobile intron into the allele. This enables non-mendelian propagation of certain introns without harming the target allele, as the introns are spliced out before functional mRNA is produced. It belongs to a large family of endonucleases all with the sequence LADLIDADG, and contains two active sites to allow simultaneous cleavage of both strands of DNA. The homing endonucleases in general are highly specific, and PI-SceI thus recognises a 31 base pair DNA sequence as its substrate, the longest specific sequence for a DNA binding protein yet discovered. This entry covers the active site which cleaves the top strand, running 5' to 3'.	Defined by 9 residues: CYS:C-1 [auth A-1]ASN:C-76 [auth A-76]THR:C-78 [auth A-78]HIS:C-79 [auth A-79]LYS:C-301 [auth A-301]LYS:C-403 [auth A-403]GLY:C-433 [auth A-433]ILE:C-434 [auth A-434]ASN:C-454 [auth A-454] \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 3.1 (PDB Primary Data)

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.