4DWR | pdb_00004dwr

RNA ligase RtcB/Mn2+ complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4dwrc1	Alpha and beta proteins (a+b)	Hypothetical protein PH1602	Hypothetical protein PH1602	Hypothetical protein PH1602	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ], (Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
C	d4dwrc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pyrococcus horikoshii ) [TaxId: 53953 ], (Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B [auth A]	d4dwra1	Alpha and beta proteins (a+b)	Hypothetical protein PH1602	Hypothetical protein PH1602	Hypothetical protein PH1602	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ], (Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B [auth A]	d4dwra2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pyrococcus horikoshii ) [TaxId: 53953 ], (Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A [auth B]	d4dwrb1	Alpha and beta proteins (a+b)	Hypothetical protein PH1602	Hypothetical protein PH1602	Hypothetical protein PH1602	automated matches	(Pyrococcus horikoshii ) [TaxId: 53953 ], (Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A [auth B]	d4dwrb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pyrococcus horikoshii ) [TaxId: 53953 ], (Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Hypothetical protein PH1602	8041707	3000172	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Hypothetical protein PH1602	8041707	3000172	SCOP2B (2022-06-29)
A [auth B]	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)
C	V-set	e4dwrC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
B [auth A]	V-set	e4dwrA1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
A [auth B]	PDEase_I	e4dwrB1	A: alpha bundles	X: Flavodoxin-like	H: Precorrin-8X methylmutase CbiC/CobH	T: Precorrin-8X methylmutase CbiC/CobH	F: PDEase_I	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.1860.10	Alpha Beta	Alpha-Beta Complex	tRNA-splicing ligase RtcB	tRNA-splicing ligase RtcB	CATH (4.3.0)
B [auth A]	3.90.1860.10	Alpha Beta	Alpha-Beta Complex	tRNA-splicing ligase RtcB	tRNA-splicing ligase RtcB	CATH (4.3.0)
A [auth B]	3.90.1860.10	Alpha Beta	Alpha-Beta Complex	tRNA-splicing ligase RtcB	tRNA-splicing ligase RtcB	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A], C	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 [auth B], B [auth A], C	IPR036844	Hint domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C	IPR036025	tRNA-splicing ligase RtcB-like superfamily	Homologous Superfamily
A [auth B], B [auth A], C	IPR030934	Intein C-terminal splicing region	Conserved Site
A [auth B], B [auth A], C	IPR006142	Intein	Domain
A [auth B], B [auth A], C	IPR004042	Intein DOD homing endonuclease, central region	Domain
A [auth B], B [auth A], C	IPR027434	Homing endonuclease	Homologous Superfamily
A [auth B], B [auth A], C	IPR006141	Intein N-terminal splicing region	PTM
A [auth B], B [auth A], C	IPR004860	Homing endonuclease, LAGLIDADG domain	Domain
A [auth B], B [auth A], C	IPR003587	Hint domain N-terminal	Domain
A [auth B], B [auth A], C	IPR001233	RNA-splicing ligase, RtcB	Family
A [auth B], B [auth A], C	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.