3KT4

Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Clavaminate synthase-like	8089989	3001848	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clavaminate synthase-like	8089987	3001848	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)
A	Ofd1_CTDD	e3kt4A1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Ofd1_CTDD	ECOD (1.6)
A	2OG-FeII_Oxy_3	e3kt4A2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
A	3.60.130.20	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF10637	Oxoglutarate and iron-dependent oxygenase degradation C-term (Ofd1_CTDD)	Oxoglutarate and iron-dependent oxygenase degradation C-term	Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory ele ...	Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PKHD-type hydroxylase TPA1	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding RNA binding organic cyclic compound binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding RNA binding organic cyclic compound binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding carbohydrate binding vitamin binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding	biological regulation regulation of biological quality regulation of translational fidelity peptidyl-proline di-hydroxylation primary metabolic process macromolecule modification peptidyl-proline hydroxylation peptidyl-amino acid modification protein hydroxylation peptidyl-proline modification metabolic process cellular process protein metabolic process macromolecule metabolic process biological regulation regulation of biological quality regulation of translational fidelity peptidyl-proline di-hydroxylation primary metabolic process macromolecule modification peptidyl-proline hydroxylation peptidyl-amino acid modification protein hydroxylation peptidyl-proline modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process cellular component disassembly protein-containing complex organization protein-containing complex disassembly translation gene expression macromolecule biosynthetic process cellular component organization biosynthetic process translational termination cellular component organization or biogenesis regulation of cellular process regulation of cellular component organization regulation of protein-containing complex disassembly regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of translational termination regulation of macromolecule metabolic process regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of biological process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process RNA destabilization nuclear-transcribed mRNA catabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A	IPR043044	TPA1/Ofd1, C-terminal	Homologous Superfamily
A	IPR051842	Ribosomal subunit uS12 prolyl hydroxylase	Family
A	IPR039558	Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain	Domain
A	IPR019601	Oxoglutarate/iron-dependent oxygenase, C-terminal degradation 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.