2O1P

Structure of yeast Poly(A) Polymerase in a somewhat closed state

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	d2o1pa1	All alpha proteins	PAP/OAS1 substrate-binding domain	PAP/OAS1 substrate-binding domain	Poly(A) polymerase, PAP, middle domain	Poly(A) polymerase, PAP, middle domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2o1pa3	Alpha and beta proteins (a+b)	Ferredoxin-like	PAP/Archaeal CCA-adding enzyme, C-terminal domain	Poly(A) polymerase, PAP, C-terminal domain	Poly(A) polymerase, PAP, C-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2o1pa2	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	Poly(A) polymerase, PAP, N-terminal domain	Poly(A) polymerase, PAP, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2o1pa4	Artifacts	Tags	Tags	Tags	C-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2o1pb1	All alpha proteins	PAP/OAS1 substrate-binding domain	PAP/OAS1 substrate-binding domain	Poly(A) polymerase, PAP, middle domain	Poly(A) polymerase, PAP, middle domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2o1pb3	Alpha and beta proteins (a+b)	Ferredoxin-like	PAP/Archaeal CCA-adding enzyme, C-terminal domain	Poly(A) polymerase, PAP, C-terminal domain	Poly(A) polymerase, PAP, C-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2o1pb2	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	Poly(A) polymerase, PAP, N-terminal domain	Poly(A) polymerase, PAP, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2o1pb4	Artifacts	Tags	Tags	Tags	C-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PAP/OAS1 substrate-binding domain-like	8035233	3000941	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8035235	3001147	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8035234	3000129	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8035235	3001147	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotidyltransferase-like	8035234	3000129	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PAP/OAS1 substrate-binding domain-like	8035233	3000941	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	PF04928	e2o1pA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: PF04928	ECOD (1.6)
A	PF04926	e2o1pA2	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: PF04926	ECOD (1.6)
A	PF20750	e2o1pA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: PF20750	ECOD (1.6)
B	PF04928	e2o1pB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: PF04928	ECOD (1.6)
B	PF04926	e2o1pB2	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: PF04926	ECOD (1.6)
B	PF20750	e2o1pB3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: PF20750	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1410.10	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain		CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.70.590	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Poly(A) polymerase predicted RNA binding domain	CATH (4.3.0)
B	1.10.1410.10	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain		CATH (4.3.0)
B	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
B	3.30.70.590	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Poly(A) polymerase predicted RNA binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04926	Poly(A) polymerase predicted RNA binding domain (PAP_RNA-bind)	Poly(A) polymerase predicted RNA binding domain	Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding [1].	Domain
A, B	PF04928	Poly(A) polymerase central domain (PAP_central)	Poly(A) polymerase central domain	In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a templa ...	In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA [1]. This entry represents the central domain.	Domain
A, B	PF01909	Nucleotidyltransferase domain (NTP_transf_2)	Nucleotidyltransferase domain	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTa ...	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Poly(A) polymerase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding poly(A) RNA polymerase activity adenylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding nucleic acid binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process nucleic acid catabolic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II termination of RNA polymerase II transcription, poly(A)-coupled nucleobase-containing compound biosynthetic process organic cyclic compound biosynthetic process termination of RNA polymerase II transcription sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle mRNA cleavage and polyadenylation specificity factor complex mRNA cleavage factor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007010	Poly(A) polymerase, RNA-binding domain	Domain
A, B	IPR011068	Nucleotidyltransferase, class I-like, C-terminal	Homologous Superfamily
A, B	IPR007012	Poly(A) polymerase, central domain	Domain
A, B	IPR014492	Poly(A) polymerase	Family
A, B	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A, B	IPR048840	Poly(A) polymerase, nucleotidyltransferase domain	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 R01GM133198.