6QH8 | pdb_00006qh8

Structure of knotted YibK from P. aeruginosa

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	d6qh8d1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d6qh8d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d6qh8d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d6qh8c1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d6qh8c3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d6qh8c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d6qh8b1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d6qh8b3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d6qh8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d6qh8a1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d6qh8a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d6qh8a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	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	8096074	3001122	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha/beta knot	8096074	3001122	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8096074	3001122	SCOP2B (2022-06-29)
A	SCOP2 Family	SpoU-like RNA 2'-O ribose methyltransferase	8096073	4002340	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta knot	8096074	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	BTB_2	e6qh8D1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: BTB_2	ECOD (v294.1)
C	BTB_2	e6qh8C1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: BTB_2	ECOD (v294.1)
B	BTB_2	e6qh8B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: BTB_2	ECOD (v294.1)
A	BTB_2	e6qh8A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: BTB_2	ECOD (v294.1)

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 (utative)
C	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (utative)
B	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (utative)
A	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00588	SpoU rRNA Methylase family (SpoU_methylase)	SpoU rRNA Methylase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	tRNA (cytidine(34)-2'-O)-methyltransferase	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity tRNA (cytidine(34)-2'-O-ribose)-methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity tRNA (cytidine(34)-2'-O-ribose)-methyltransferase activity catalytic activity RNA binding binding nucleic acid binding tRNA (uridine) methyltransferase activity tRNA (5-carboxymethylaminomethyluridine(34)-2'-O-ribose)-methyltransferase activity identical protein binding protein binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing wobble position uridine ribose methylation tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing wobble position uridine ribose methylation tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation wobble position ribose methylation tRNA metabolic process tRNA nucleoside ribose methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation wobble position cytosine ribose methylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001537	tRNA/rRNA methyltransferase, SpoU type	Domain
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	IPR016914	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL	Family

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.