1VHK | pdb_00001vhk

Crystal structure of an hypothetical protein

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)
D	d1vhkd1	All beta proteins	PUA domain-like	PUA domain-like	YggJ N-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1vhkd2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YggJ C-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1vhkc1	All beta proteins	PUA domain-like	PUA domain-like	YggJ N-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1vhkc2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YggJ C-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1vhkb1	All beta proteins	PUA domain-like	PUA domain-like	YggJ N-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1vhkb2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YggJ C-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1vhka1	All beta proteins	PUA domain-like	PUA domain-like	YggJ N-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1vhka2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YggJ C-terminal domain-like	Hypothetical protein YqeU	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	alpha/beta knot	8035814	3001122	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PUA domain-like	8035811	3001015	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha/beta knot	8035814	3001122	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8035814	3001122	SCOP2B (2022-06-29)
A	SCOP2 Family	RsmE N-terminal domain-like	8023431	4000398	SCOP2 (2022-06-29)
A	SCOP2 Family	RmsE C-terminal domain-like	8023434	4000479	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PUA domain-like	8035811	3001015	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta knot	8035814	3001122	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)
D	RecU	e1vhkD1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (develop294)
C	Peptidase_S46, Trypsin_2	e1vhkC1	A: alpha bundles	X: Cloacin translocation domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (develop294)
C	RecU	e1vhkC2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (develop294)
B	Peptidase_S46, Trypsin_2	e1vhkB1	A: alpha bundles	X: Cloacin translocation domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (develop294)
B	RecU	e1vhkB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (develop294)
A	PUA_4	e1vhkA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA_4	ECOD (develop294)
A	Methyltrans_RNA	e1vhkA2	A: alpha bundles	X: alpha/beta knot	H: alpha/beta knot	T: alpha/beta knot	F: Methyltrans_RNA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
C	2.40.240.20	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
C	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	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, C, D	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, C, D	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, C, D	Hypothetical protein yqeU	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, C, D	IPR015947	PUA-like superfamily	Homologous Superfamily
A, B, C, D	IPR046886	Ribosomal RNA small subunit methyltransferase E, methyltransferase domain	Domain
A, B, C, D	IPR006700	Ribosomal RNA small subunit methyltransferase E	Family
A, B, C, D	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A, B, C, D	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A, B, C, D	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.