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)
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)
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)

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)
D [auth A]	SCOP2B Superfamily	Rnp2-like	8065987	3000630	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)

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)
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)
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)

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)
D [auth A]	3.30.70.3250	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribonuclease P, Pop5 subunit	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 5'-end processing metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 5'-end processing metabolic process cellular process macromolecule metabolic process RNA processing tRNA 5'-leader removal tRNA 5'-end processing	cellular anatomical structure intracellular anatomical structure cytoplasm 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	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 5'-end processing metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 5'-end processing metabolic process cellular process macromolecule metabolic process RNA processing tRNA 5'-leader removal tRNA 5'-end processing	cellular anatomical structure intracellular anatomical structure cytoplasm 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 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.