3WZ0

On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis

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 [auth E]	d3wz0e_	Alpha and beta proteins (a/b)	7-stranded beta/alpha barrel	PHP domain-like	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
B [auth F]	d3wz0f_	Alpha and beta proteins (a/b)	7-stranded beta/alpha barrel	PHP domain-like	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
C	d3wz0c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Rnp2-like	Rpp14/Pop5-like	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
D [auth A]	d3wz0a_	Alpha and beta proteins (a+b)	Ferredoxin-like	Rnp2-like	Rpp14/Pop5-like	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth E]	SCOP2 Family	RNase P subunit p30	8066106	4002021	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	PHP domain-like	8066107	3000312	SCOP2 (2022-06-29)
B [auth F]	SCOP2B Superfamily	PHP domain-like	8066107	3000312	SCOP2B (2022-06-29)
C	SCOP2 Family	Rpp14/Pop5-like	8065986	4001975	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Rnp2-like	8065987	3000630	SCOP2 (2022-06-29)
D [auth A]	SCOP2B Superfamily	Rnp2-like	8065987	3000630	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)
A [auth E]	RNase_P_p30	e3wz0E1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RNase_P_p30	ECOD (1.6)
B [auth F]	RNase_P_p30	e3wz0F1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RNase_P_p30	ECOD (1.6)
C	RNase_P_Rpp14	e3wz0C1	A: a+b two layers	X: Alpha-beta plaits	H: Rpp14/Pop5-like (From Topology)	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (1.6)
D [auth A]	RNase_P_Rpp14	e3wz0A1	A: a+b two layers	X: Alpha-beta plaits	H: Rpp14/Pop5-like (From Topology)	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth E]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
B [auth F]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
C	3.30.70.3250	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribonuclease P, Pop5 subunit	CATH (4.3.0)
D [auth A]	3.30.70.3250	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribonuclease P, Pop5 subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth F]	PF01876	RNase P subunit p30 (RNase_P_p30)	RNase P subunit p30	This protein is part of the RNase P complex that is involved in tRNA maturation [1].	Domain
C, D [auth A]	PF01900	Rpp14/Pop5 family (RNase_P_Rpp14)	Rpp14/Pop5 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth F]	Ribonuclease P protein component 3	tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing tRNA 5'-end processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing tRNA 5'-end processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process nucleic acid catabolic process RNA 5'-end processing metabolic process cellular process macromolecule metabolic process tRNA 5'-leader removal	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex endoribonuclease complex catalytic complex ribonuclease P complex ribonucleoprotein complex intracellular protein-containing complex endonuclease complex
C, D [auth A]	Ribonuclease P protein component 2	tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing tRNA 5'-end processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing tRNA 5'-end processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process nucleic acid catabolic process RNA 5'-end processing metabolic process cellular process macromolecule metabolic process tRNA 5'-leader removal	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex endoribonuclease complex catalytic complex ribonuclease P complex ribonucleoprotein complex intracellular protein-containing complex endonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], B [auth F]	IPR016195	Polymerase/histidinol phosphatase-like	Homologous Superfamily
A [auth E], B [auth F]	IPR023539	Ribonuclease P, protein component 3, archaeal	Family
A [auth E], B [auth F]	IPR002738	RNase P subunit p30	Family
C, D [auth A]	IPR002759	RNase P subunit Pop5/Rpp14/Rnp2-like	Family
C, D [auth A]	IPR016434	Ribonuclease P protein subunit Rnp2, archaea	Family
C, D [auth A]	IPR038085	RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily	Homologous Superfamily

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.