2PGG

Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1

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	d2pgga1	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	Gumboro virus (Infectious bursal disease virus ) [TaxId: 10995 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	RNA-dependent RNA-polymerase	8023246	4002808	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035626	3001272	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	Birna_RdRp_2nd	e2pggA1	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: Birna_RdRp_2nd	ECOD (1.6)
A	Birna_RdRp_3rd	e2pggA2	A: alpha complex topology	X: Sigma2 domain-like	H: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase (From Topology)	T: C-terminal bundle domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_3rd	ECOD (1.6)
A	Birna_RdRp_1st	e2pggA3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: 'palm' domain in birnaviruse RNA-dependent RNA polymerase	F: Birna_RdRp_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1730.10	Alpha Beta	Alpha-Beta Complex	Infectious bursal virus vp1 polymerase fold	Infectious bursal virus vp1 polymerase domain	CATH (4.3.0)
A	1.10.287.540	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A	6.10.140.300	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	1.10.1740.80	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04197	Birnavirus RNA dependent RNA polymerase (VP1), palm domain (Birna_RdRp_palm)	Birnavirus RNA dependent RNA polymerase (VP1), palm domain	Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all cla ...	Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [1,2]. The catalytic motifs are arranged in a permuted order in sequence [2].	Domain
A	PF20488	Birnavirus RNA dependent RNA polymerase (VP1), thumb domain (Birna_VP1_thumb)	Birnavirus RNA dependent RNA polymerase (VP1), thumb domain	Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteristic permuted order, thus, it adopts a ...	Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteristic permuted order, thus, it adopts a unique active site topology [2,3]. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [1,2,3]. This entry covers the thumb domain of RdRP from Birnaviruses.	Domain
A	PF20489	Birnavirus RNA dependent RNA polymerase (VP1), C-terminal (Birna_RdRp_C)	Birnavirus RNA dependent RNA polymerase (VP1), C-terminal	Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all clas ...	Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [1]. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site [2,3]. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain [2], which may function to prevent back-primed RNA synthesis during protein priming.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RNA-directed RNA polymerase	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	viral genome replication viral process viral life cycle	virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046750	RNA-directed RNA polymerase, C-terminal, birnavirus	Domain
A	IPR046812	RNA-directed RNA polymerase, palm domain superfamily, Birnavirus	Homologous Superfamily
A	IPR007100	Birnavirus RNA-directed RNA polymerase, palm domain	Domain
A	IPR046752	RNA-directed RNA polymerase, thumb domain, birnavirus	Domain
A	IPR046813	RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus	Homologous Superfamily
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR046814	RNA-directed RNA polymerase, C-terminal domain superfamily, Avibirnavirus	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.