3ER8 | pdb_00003er8

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA

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)
B	d3er8b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	mRNA cap methylase	Polymerase regulatory subunit VP39	(Vaccinia virus WR ) [TaxId: 10254 ],	SCOPe (2.08)
A	d3er8a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	mRNA cap methylase	Polymerase regulatory subunit VP39	(Vaccinia virus WR ) [TaxId: 10254 ],	SCOPe (2.08)
D	d3er8d_	Multi-domain proteins (alpha and beta)	Poly(A) polymerase catalytic subunit-like	Poly(A) polymerase catalytic subunit-like	Poxvirus poly(A) polymerase catalytic subunit-like	automated matches	(Vaccinia virus WR ) [TaxId: 10254 ],	SCOPe (2.08)
C	d3er8c_	Multi-domain proteins (alpha and beta)	Poly(A) polymerase catalytic subunit-like	Poly(A) polymerase catalytic subunit-like	Poxvirus poly(A) polymerase catalytic subunit-like	automated matches	(Vaccinia virus WR ) [TaxId: 10254 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032283	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032283	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Poxvirus poly(A) polymerase N-terminal domain-like	8055708	3002298	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotidyltransferase-like	8055710	3000129	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Poly(A) polymerase C-terminal domain-like	8032899	3001629	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Poxvirus poly(A) polymerase N-terminal domain-like	8055708	3002298	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotidyltransferase-like	8055710	3000129	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Poly(A) polymerase C-terminal domain-like	8032899	3001629	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)
B	Spt5-NGN	e3er8B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Spt5-NGN	ECOD (v294.1)
A	PARP_regulatory	e3er8A1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: FAD-dependent thiol oxidase	T: FAD-dependent thiol oxidase	F: PARP_regulatory	ECOD (v294.1)
D	EB1	e3er8D4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: EB1	ECOD (v294.1)
C	PARP_regulatory	e3er8C1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: FAD-dependent thiol oxidase	T: FAD-dependent thiol oxidase	F: PARP_regulatory	ECOD (v294.1)
C	FTO_NTD	e3er8C4	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: FTO_NTD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	1.20.1270.320	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
D	3.30.460.60	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
C	1.20.1270.320	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
C	3.30.460.60	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01358	Poly A polymerase regulatory subunit (PARP_regulatory)	Poly A polymerase regulatory subunit		Domain
C, D	PF03296	Poxvirus poly(A) polymerase nucleotidyltransferase domain (Pox_polyA_pol)	Poxvirus poly(A) polymerase nucleotidyltransferase domain		Domain
C, D	PF12629	Poxvirus poly(A) polymerase C-terminal domain (Pox_polyA_pol_C)	Poxvirus poly(A) polymerase C-terminal domain	This domain is found at the C-terminus of the pox virus PolyA polymerase protein [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase	RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding binding nucleic acid binding	methylation metabolic process cellular process 7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process methylation metabolic process cellular process 7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping 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 5'-end processing RNA processing macromolecule metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process regulation of mRNA processing regulation of biological process mRNA 3'-end processing regulation of mRNA 3'-end processing biological regulation regulation of macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process	virion component
C, D	Poly(A) polymerase catalytic subunit	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding poly(A) RNA polymerase activity adenylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process RNA processing	-
E	RNA/DNA chimera 5'-D(CPCP)R(UPUP)D(C)-3'	-	-	-
F	RNA/DNA chimera 5'-R(PUPUP*)D(C)-3'	-	-	-
G, H	RNA/DNA chimera 5'-D(PCP)R(UP*U)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000176	mRNA methyltransferase-like	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR030375	Poxvirus cap-specific nucleoside 2-O-methyltransferase	Family
A, B	IPR025804	Poxvirus/kinetoplastid-type cap-specific nucleoside 2-O-methyltransferase	Family
C, D	IPR038337	Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR024397	Poxvirus poly(A) polymerase, catalytic subunit, C-terminal	Domain
C, D	IPR004976	Poly(A) polymerase catalytic subunit, Poxvirus	Family
C, D	IPR038419	Poly(A) polymerase, nucleotidyltransferase domain superfamily, Poxvirus	Homologous Superfamily
C, D	IPR024231	Poly(A) polymerase, nucleotidyltransferase domain, Poxvirus	Domain
C, D	IPR037265	Poly(A) polymerase catalytic subunit superfamily	Homologous Superfamily
C, D	IPR024398	Poxvirus poly(A) polymerase, catalytic subunit, N-terminal	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.