3ZQ4 | pdb_00003zq4

Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Lactamase_B_6_1	e3zq4A2	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_6_1	ECOD (1.6)
A	RnjA	e3zq4A1	A: a+b complex topology	X: Flagellar protein FlgA N-terminal domain-like	H: RNase J C-terminal domain (From Topology)	T: RNase J C-terminal domain	F: RnjA	ECOD (1.6)
A	MG423	e3zq4A3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MG423	ECOD (1.6)
B [auth C]	Lactamase_B_6_1	e3zq4C3	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_6_1	ECOD (1.6)
B [auth C]	RnjA	e3zq4C1	A: a+b complex topology	X: Flagellar protein FlgA N-terminal domain-like	H: RNase J C-terminal domain (From Topology)	T: RNase J C-terminal domain	F: RnjA	ECOD (1.6)
B [auth C]	MG423	e3zq4C2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MG423	ECOD (1.6)
C [auth D]	Lactamase_B_6_1	e3zq4D3	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_6_1	ECOD (1.6)
C [auth D]	RnjA	e3zq4D2	A: a+b complex topology	X: Flagellar protein FlgA N-terminal domain-like	H: RNase J C-terminal domain (From Topology)	T: RNase J C-terminal domain	F: RnjA	ECOD (1.6)
C [auth D]	MG423	e3zq4D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MG423	ECOD (1.6)
D [auth E]	Lactamase_B_6_1	e3zq4E3	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_6_1	ECOD (1.6)
D [auth E]	RnjA	e3zq4E1	A: a+b complex topology	X: Flagellar protein FlgA N-terminal domain-like	H: RNase J C-terminal domain (From Topology)	T: RNase J C-terminal domain	F: RnjA	ECOD (1.6)
D [auth E]	MG423	e3zq4E2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MG423	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
A	3.40.50.10710	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Metallo-hydrolase/oxidoreductase	CATH (4.3.0)
A	3.10.20.580	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B [auth C]	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
B [auth C]	3.40.50.10710	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Metallo-hydrolase/oxidoreductase	CATH (4.3.0)
B [auth C]	3.10.20.580	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C [auth D]	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
C [auth D]	3.40.50.10710	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Metallo-hydrolase/oxidoreductase	CATH (4.3.0)
C [auth D]	3.10.20.580	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
D [auth E]	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
D [auth E]	3.40.50.10710	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Metallo-hydrolase/oxidoreductase	CATH (4.3.0)
D [auth E]	3.10.20.580	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth D], D [auth E]	PF07521	Zn-dependent metallo-hydrolase RNA specificity domain (RMMBL)	Zn-dependent metallo-hydrolase RNA specificity domain	-	Motif
A, B [auth C], C [auth D], D [auth E]	PF17770	Ribonuclease J C-terminal domain (RNase_J_C)	Ribonuclease J C-terminal domain	This domain is found at the C-terminus of Ribonuclease J proteins. Its function is unknown, but deletion of this domain causes dissociation to monomers [2].	Domain
A, B [auth C], C [auth D], D [auth E]	PF22505	Ribonuclease J, beta-CASP domain (RNase_J_b_CASP)	Ribonuclease J, beta-CASP domain	This domain is found in Ribonuclease J from Thermus thermophilus (RNaseJ) and similar bacterial proteins. RNaseJ is an RNase that has endonuclease and possibly 5'-3' exonuclease activity. It is probably involved in maturation of rRNA and in some orga ...	This domain is found in Ribonuclease J from Thermus thermophilus (RNaseJ) and similar bacterial proteins. RNaseJ is an RNase that has endonuclease and possibly 5'-3' exonuclease activity. It is probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. This protein shows three globular domains: the beta lactamase core (formed by two separate regions, Pfam:PF12706 and Pfam:PF07521), the beta-CASP (this entry) and the C-terminal domain (Pfam: PF17770). This domain consists of a central five-stranded parallel beta-sheet that is surrounded by five alpha-helices [1,2].	Domain
A, B [auth C], C [auth D], D [auth E]	PF00753	Metallo-beta-lactamase superfamily (Lactamase_B)	Metallo-beta-lactamase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth D], D [auth E]	RIBONUCLEASE J 1	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity 5'-3' RNA exonuclease activity 5'-3' exonuclease activity RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity exonuclease activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity 5'-3' RNA exonuclease activity 5'-3' exonuclease activity RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity exonuclease activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding identical protein binding protein binding	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process mRNA processing mRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth D], D [auth E]	IPR001279	Metallo-beta-lactamase	Domain
A, B [auth C], C [auth D], D [auth E]	IPR001587	Ribonuclease J, conserved site	Conserved Site
A, B [auth C], C [auth D], D [auth E]	IPR055132	Ribonuclease J, beta-CASP domain	Domain
A, B [auth C], C [auth D], D [auth E]	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain	Domain
A, B [auth C], C [auth D], D [auth E]	IPR004613	Ribonuclease J	Family
A, B [auth C], C [auth D], D [auth E]	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, B [auth C], C [auth D], D [auth E]	IPR030854	Ribonuclease J, bacteria	Family
A, B [auth C], C [auth D], D [auth E]	IPR041636	Ribonuclease J, C-terminal	Domain
A, B [auth C], C [auth D], D [auth E]	IPR042173	Ribonuclease J, domain 2	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.