8DCD | pdb_00008dcd

RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Hypothetical protein PH1602	8041707	3000172	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hypothetical protein PH1602	8041707	3000172	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)
B	PDEase_I	e8dcdB1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PDEase_I	ECOD (develop294)
A	PDEase_I	e8dcdA1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PDEase_I	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	tRNA-splicing ligase RtcB	DNA binding binding nucleic acid binding ligase activity, forming phosphoric ester bonds RNA ligase (ATP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity RNA ligase (GTP) activity cation binding manganese ion binding transition metal ion binding DNA binding binding nucleic acid binding ligase activity, forming phosphoric ester bonds RNA ligase (ATP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity RNA ligase (GTP) activity cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding hydrolase activity endonuclease activity nuclease activity guanyl nucleotide binding nucleotide binding GMP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding GTP binding purine ribonucleoside triphosphate binding	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 nucleobase-containing compound 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 nucleobase-containing compound metabolic process DNA recombination DNA metabolic process nucleic acid metabolic process intron homing RNA metabolic process nucleobase-containing compound biosynthetic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing RNA splicing RNA splicing, via endonucleolytic cleavage and ligation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036844	Hint domain superfamily	Homologous Superfamily
A, B	IPR036025	tRNA-splicing ligase RtcB-like superfamily	Homologous Superfamily
A, B	IPR030934	Intein C-terminal splicing region	Conserved Site
A, B	IPR006142	Intein	Domain
A, B	IPR004042	Intein DOD homing endonuclease, central region	Domain
A, B	IPR027434	Homing endonuclease	Homologous Superfamily
A, B	IPR006141	Intein N-terminal splicing region	PTM
A, B	IPR004860	Homing endonuclease, LAGLIDADG domain	Domain
A, B	IPR003587	Hint domain N-terminal	Domain
A, B	IPR001233	RNA-splicing ligase, RtcB	Family
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.