4OHY

C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Clp1 N-terminal domain-like	8045805	4004697	SCOP2 (2022-06-29)
A	SCOP2 Family	Clp1 PNK domain-like	8045807	4004698	SCOP2 (2022-06-29)
A	SCOP2 Family	mRNA cleavage and polyadenylation factor CLP1, C-terminal domain-like	8048771	4006213	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	cAMP-binding domain-like	8091494	3000084	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Simibi-like P-loop NTPases	8091493	3002018	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Clp1 C-terminal domain-like	8091492	3002513	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	Clp1	e4ohyA2	A: beta barrels	X: Protein CLP1 C-terminal domain (From Topology)	H: Protein CLP1 C-terminal domain (From Topology)	T: Protein CLP1 C-terminal domain	F: Clp1	ECOD (1.6)
A	CLP1_N	e4ohyA3	A: beta sandwiches	X: jelly-roll	H: Protein CLP1 jelly-roll domain (From Topology)	T: Protein CLP1 jelly-roll domain	F: CLP1_N	ECOD (1.6)
A	CLP1_P	e4ohyA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: CLP1_P	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.1030	Mainly Beta	Sandwich	Jelly Rolls	Clp1, DNA binding domain	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.330	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF06807	Pre-mRNA cleavage complex II protein Clp1 (Clp1)	Pre-mRNA cleavage complex II protein Clp1	-	Family
A	PF16573	N-terminal beta-sandwich domain of polyadenylation factor (CLP1_N)	N-terminal beta-sandwich domain of polyadenylation factor	-	Family
A	PF16575	mRNA cleavage and polyadenylation factor CLP1 P-loop (CLP1_P)	mRNA cleavage and polyadenylation factor CLP1 P-loop	CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or g ...	CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or guanine nucleotide [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein clpf-1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process RNA splicing tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation RNA splicing, via endonucleolytic cleavage and ligation tRNA processing	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle
B	RNA (5'-R(GPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR032324	Clp1, N-terminal beta-sandwich domain	Domain
A	IPR032319	Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain	Domain
A	IPR038238	Clp1, C-terminal domain superfamily	Homologous Superfamily
A	IPR038239	Clp1, N-terminal beta-sandwich domain superfamily	Homologous Superfamily
A	IPR045116	Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3	Family
A	IPR010655	Pre-mRNA cleavage complex subunit Clp1, C-terminal	Domain
A	IPR028606	Polyribonucleotide 5-hydroxyl-kinase Clp1	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.