1VHY | pdb_00001vhy

Crystal structure of Haemophilus influenzae protein HI0303, Pfam DUF558

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	d1vhyb1	All beta proteins	PUA domain-like	PUA domain-like	YggJ N-terminal domain-like	Hypothetical protein HI0303	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1vhyb2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YggJ C-terminal domain-like	Hypothetical protein HI0303	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1vhyb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1vhya1	All beta proteins	PUA domain-like	PUA domain-like	YggJ N-terminal domain-like	Hypothetical protein HI0303	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1vhya2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YggJ C-terminal domain-like	Hypothetical protein HI0303	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1vhya3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PUA domain-like	8033719	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8033721	3001122	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8033719	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha/beta knot	8033721	3001122	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	Peptidase_S46, Trypsin_2	e1vhyB1	A: alpha bundles	X: Cloacin translocation domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (develop294)
B	RecU	e1vhyB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (develop294)
A	Peptidase_S46, Trypsin_2	e1vhyA1	A: alpha bundles	X: Cloacin translocation domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (develop294)
A	RecU	e1vhyA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.240.20	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
B	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
A	2.40.240.20	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
A	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20260	RNA methyltransferase PUA domain (PUA_4)	RNA methyltransferase PUA domain	RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation [1][2].	Domain
A, B	PF04452	RNA methyltransferase domain (Methyltrans_RNA)	RNA methyltransferase domain	RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation [1][2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hypothetical protein HI0303	RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity rRNA (uridine-N3-)-methyltransferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (uridine) methyltransferase activity N-methyltransferase activity methyltransferase activity catalytic activity	ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process rRNA base methylation RNA methylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015947	PUA-like superfamily	Homologous Superfamily
A, B	IPR046886	Ribosomal RNA small subunit methyltransferase E, methyltransferase domain	Domain
A, B	IPR006700	Ribosomal RNA small subunit methyltransferase E	Family
A, B	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A, B	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A, B	IPR046887	Ribosomal RNA small subunit methyltransferase E, PUA-like 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.