3DH3 | pdb_00003dh3

Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth D]	Methyltransf_25	e3dh3D1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Methyltransf_25	ECOD (develop294)
E [auth C]	Methyltransf_25	e3dh3C1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Methyltransf_25	ECOD (develop294)
C [auth B]	Methyltransf_25	e3dh3B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Methyltransf_25	ECOD (develop294)
A	Aldo_ket_red	e3dh3A1	A: alpha bundles	X: Alpha-beta plaits	H: CheC-like	T: CheC-like	F: Aldo_ket_red	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth D]	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
G [auth D]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
E [auth C]	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
E [auth C]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
C [auth B]	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
C [auth B]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
A	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
A	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D]	PF00849	RNA pseudouridylate synthase (PseudoU_synth_2)	RNA pseudouridylate synthase	-	Family
A, C [auth B], E [auth C], G [auth D]	PF01479	S4 domain (S4)	S4 domain	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], D [auth F], F [auth G], H	stem loop fragment of E. Coli 23S RNA	-	-	-
A, C [auth B], E [auth C], G [auth D]	Ribosomal large subunit pseudouridine synthase F	isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid rRNA pseudouridine synthase activity 23S rRNA pseudouridine(2604) synthase activity tRNA pseudouridine synthase activity catalytic activity, acting on a tRNA RNA binding binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis 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 pseudouridine synthesis ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis 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 pseudouridine synthesis rRNA pseudouridine synthesis primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process tRNA pseudouridine synthesis tRNA modification tRNA metabolic process tRNA processing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C], G [auth D]	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR002942	RNA-binding S4 domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR020094	Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR050343	Ribosomal RNA Pseudouridine Synthase RsuA	Family
A, C [auth B], E [auth C], G [auth D]	IPR000748	Pseudouridine synthase, RsuA/RluB/E/F	Family
A, C [auth B], E [auth C], G [auth D]	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR006145	Pseudouridine synthase, RsuA/RluA-like	Domain
A, C [auth B], E [auth C], G [auth D]	IPR018496	Pseudouridine synthase, RsuA/RluB/E/F, conserved site	Conserved Site
A, C [auth B], E [auth C], G [auth D]	IPR042092	Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.