1LWT | pdb_00001lwt

Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)

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)
C [auth A]	d1lwta1	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]	d1lwta2	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	Homing endonucleases	8035772	3000266	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Homing endonucleases	8035774	3000266	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Hedgehog/intein (Hint) domain	8042232	3001979	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]		e1lwtA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: PABC(PABP) domain	H: PABC(PABP) domain	T: PABP	F:	ECOD (20:10:01)
C [auth A]		e1lwtA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)

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]	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
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 monoatomic ion transmembrane transporter activity transporter activity transmembrane 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 monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity hydrolase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 catalytic activity, acting on a nucleic acid	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process metabolic process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process DNA recombination 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 gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process protein splicing Golgi lumen acidification vacuolar acidification	ATPase dependent transmembrane transport complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure membrane protein complex proton-transporting V-type ATPase complex proton-transporting V-type ATPase, V1 domain transporter complex vacuolar proton-transporting V-type ATPase, V1 domain intracellular organelle cellular anatomical structure bounding membrane of organelle proton-transporting two-sector ATPase complex ATPase dependent transmembrane transport complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure membrane protein complex proton-transporting V-type ATPase complex proton-transporting V-type ATPase, V1 domain transporter complex vacuolar proton-transporting V-type ATPase, V1 domain intracellular organelle cellular anatomical structure bounding membrane of organelle proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain vacuolar membrane catalytic complex membrane vacuole intracellular membrane-bounded organelle vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex organelle cytoplasm organelle membrane storage vacuole lytic vacuole fungal-type vacuole lytic vacuole membrane fungal-type vacuole membrane Golgi membrane Golgi apparatus endomembrane system
B [auth C]	PI-SceI DNA substrate bottom strand	-	-	-
A [auth B]	PI-SceI DNA substrate top strand	-	-	-

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]	IPR004042	Intein DOD homing endonuclease, central region	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]	IPR031686	ATPsynthase alpha/beta subunit, barrel-sandwich domain	Domain
C [auth A]	IPR006141	Intein N-terminal splicing region	PTM
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]	IPR030934	Intein C-terminal splicing region	Conserved Site
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]	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
C [auth A]	IPR003587	Hint domain N-terminal	Domain
C [auth A]	IPR007869	Homing endonuclease PI-Sce	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.