5ULJ | pdb_00005ulj

Crystal structure of Scheffersomyces stipitis Rai1 in complex with (3'-NADP)+ and calcium ion

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	PDZ	e5uljA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PDZ	ECOD (v294.1)
D	PDZ	e5uljD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PDZ	ECOD (v294.1)
C	PDZ	e5uljC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PDZ	ECOD (v294.1)
B	PDZ	e5uljB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PDZ	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08652	RAI1 like PD-(D/E)XK nuclease (RAI1)	RAI1 like PD-(D/E)XK nuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RAI1	phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity binding nucleoside phosphate binding nucleotide binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding pyrophosphatase activity mRNA 5'-diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides enzyme regulator activity molecular function regulator activity RNA binding nucleic acid binding cation binding ion binding metal ion binding	nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process RNA catabolic process termination of RNA polymerase II transcription, poly(A)-coupled nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process termination of RNA polymerase II transcription regulation of cellular process negative regulation of biological process deadenylation-independent decapping of nuclear-transcribed mRNA negative regulation of cellular process mRNA methylguanosine-cap decapping nuclear-transcribed mRNA catabolic process, deadenylation-independent decay negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process mRNA metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process RNA decapping NAD-cap decapping mRNA processing RNA processing protein-containing complex disassembly regulation of protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of primary 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 cellular component disassembly positive regulation of RNA metabolic process regulation of termination of DNA-templated transcription regulation of DNA-templated transcription regulation of termination of RNA polymerase II transcription regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of termination of DNA-templated transcription cellular component organization positive regulation of biosynthetic process positive regulation of termination of RNA polymerase II transcription cellular component organization or biogenesis positive regulation of protein-containing complex disassembly positive regulation of cellular process regulation of RNA biosynthetic process protein-containing complex organization positive regulation of RNA biosynthetic process ribonucleoprotein complex biogenesis rRNA processing cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis ribosome biogenesis rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA ribosomal large subunit biogenesis maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of LSU-rRNA	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle exoribonuclease complex transferase complex endonuclease complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle exoribonuclease complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex cytoplasm cytosol intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR039039	RAI1-like family	Family
A, B, C, D	IPR013961	RAI1-like	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.

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