1DQ3 | pdb_00001dq3

CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI

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)
A	d1dq3a1	All beta proteins	Hedgehog/intein (Hint) domain	Hedgehog/intein (Hint) domain	Intein (protein splicing domain)	PI-Pfui intein	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1dq3a2	Alpha and beta proteins (a+b)	dsRBD-like	YcfA/nrd intein domain	PI-Pfui intein middle domain	PI-Pfui intein middle domain	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1dq3a3	Alpha and beta proteins (a+b)	Homing endonuclease-like	Homing endonucleases	Intein endonuclease	PI-Pfui intein	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PI-Pfui intein middle domain	8022726	4001187	SCOP2 (2022-06-29)
A	SCOP2 Family	Intein endonuclease	8023398	4001703	SCOP2 (2022-06-29)
A	SCOP2 Family	Intein endonuclease	8023400	4001703	SCOP2 (2022-06-29)
A	SCOP2 Family	Intein (protein splicing domain)	8030769	4002988	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YcfA/nrd intein domain	8035106	3001014	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Homing endonucleases	8035778	3000266	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Homing endonucleases	8035780	3000266	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Hedgehog/intein (Hint) domain	8043148	3001979	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)
A	Intein_splicing	e1dq3A1	A: beta complex topology	X: Hedgehog/intein (From Homology)	H: Hedgehog/intein	T: Hint	F: Intein_splicing	ECOD (1.6)
A	Endonuc_subdom	e1dq3A2	A: a+b two layers	X: Homing endonucleases-like	H: Homing endonucleases (From Topology)	T: Homing endonucleases	F: Endonuc_subdom	ECOD (1.6)
A	LAGLIDADG_3	e1dq3A3	A: a+b two layers	X: Homing endonucleases-like	H: Homing endonucleases (From Topology)	T: Homing endonucleases	F: LAGLIDADG_3	ECOD (1.6)
A	Stirrup	e1dq3A4	A: a+b two layers	X: dsRBD-like	H: PI-Pfui intein middle domain (From Topology)	T: PI-Pfui intein middle domain	F: Stirrup	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.16.10	Mainly Beta	Beta Complex	Endonuclease - Pi-scei	Chain A, domain 1	CATH (4.3.0)
A	3.30.160.90	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain		CATH (4.3.0)
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
A	PF14528	LAGLIDADG-like domain (LAGLIDADG_3)	LAGLIDADG-like domain	This domain is part of the LAGLIDADG superfamily [1].	Domain
A	PF14890	Intein splicing domain (Intein_splicing)	Intein splicing domain	-	Family
A	PF09061	Stirrup (Stirrup)	Stirrup	The Stirrup domain, found in the prokaryotic protein ribonucleotide reductase, has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a pred ...	The Stirrup domain, found in the prokaryotic protein ribonucleotide reductase, has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface [1].	Domain
A	PF09062	PI-PfuI Endonuclease subdomain (Endonuc_subdom)	PI-PfuI Endonuclease subdomain	The endonuclease subdomain, found in the prokaryotic protein ribonucleotide reductase, assumes an alpha-beta-beta-alpha-beta-beta-alpha-alpha topology. The four stranded beta-sheet forms a saddle-shaped surface and assembles together through an inter ...	The endonuclease subdomain, found in the prokaryotic protein ribonucleotide reductase, assumes an alpha-beta-beta-alpha-beta-beta-alpha-alpha topology. The four stranded beta-sheet forms a saddle-shaped surface and assembles together through an interface made of alpha-helices. The presence of 14 basic residues on the surface of the beta-sheets suggests that this large groove may be involved in DNA binding [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ENDONUCLEASE	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 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 ribonucleoside-diphosphate reductase activity oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor catalytic activity vitamin binding cobalamin binding tetrapyrrole binding endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid	intein-mediated protein splicing primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process protein splicing nucleoside phosphate metabolic process intein-mediated protein splicing primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process protein splicing nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process small molecule metabolic process phosphorus metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036844	Hint domain superfamily	Homologous Superfamily
A	IPR013509	Ribonucleotide reductase large subunit, N-terminal	Domain
A	IPR030934	Intein C-terminal splicing region	Conserved Site
A	IPR015146	Ribonucleotide reductase, stirrup	Domain
A	IPR006142	Intein	Domain
A	IPR004042	Intein DOD homing endonuclease, central region	Domain
A	IPR027434	Homing endonuclease	Homologous Superfamily
A	IPR005144	ATP-cone domain	Domain
A	IPR006141	Intein N-terminal splicing region	PTM
A	IPR008926	Ribonucleotide reductase R1 subunit, N-terminal	Homologous Superfamily
A	IPR004860	Homing endonuclease, LAGLIDADG domain	Domain
A	IPR003587	Hint domain N-terminal	Domain
A	IPR013344	Ribonucleotide reductase, adenosylcobalamin-dependent	Family
A	IPR000788	Ribonucleotide reductase large subunit, C-terminal	Domain
A	IPR050862	Ribonucleoside diphosphate reductase class-2	Family
A	IPR015147	PI-PfuI intein endonuclease, subdomain	Domain
A	IPR003586	Hint domain C-terminal	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.