5LM5 | pdb_00005lm5

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM2 peptide (region 435-451)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	SCOP2B Superfamily	ARM repeat-like	8053885	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8053885	3000116	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)
B	Sel1	e5lm5B1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (develop294)
A	Sel1	e5lm5A1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	mRNA decapping protein 2	RNA binding binding nucleic acid binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding chromatin binding hydrolase activity catalytic activity pyrophosphatase activity RNA binding binding nucleic acid binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding chromatin binding hydrolase activity catalytic activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of transcription initiation by RNA polymerase II biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process negative regulation of biological process post-transcriptional regulation of gene expression regulation of biological quality RNA catabolic process mRNA catabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping negative regulation of macromolecule metabolic process nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA 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 component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay nuclear-transcribed mRNA catabolic process, nonsense-mediated decay mRNA processing RNA processing	cellular anatomical structure cytoplasmic side of membrane membrane side of membrane protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle cytoplasm cellular anatomical structure cytoplasmic side of membrane membrane side of membrane protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle cytoplasm supramolecular complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, B	DNA topoisomerase 2-associated protein PAT1	RNA binding binding nucleic acid binding mRNA binding chromatin binding	regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA regulation of metabolic process RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic 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 cellular process regulation of mRNA metabolic process protein biosynthetic process translational initiation protein metabolic process regulation of translational initiation regulation of protein metabolic process translation regulation of translation ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis formation of translation preinitiation complex protein-containing complex organization cytoplasmic translation cytoplasmic translational initiation cell division cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to glucose starvation cellular response to starvation negative regulation of translation negative regulation of protein metabolic process negative regulation of translational initiation organelle organization organelle assembly P-body assembly membraneless organelle assembly nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule chromosome chromosomal region kinetochore intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit ribosomal subunit cytosolic ribosome ribonucleoprotein complex ribosome cytosol P-body Lsm1-7-Pat1 complex Sm-like protein family complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR036189	mRNA decapping protein 2, Box A domain superfamily	Homologous Superfamily
C, D	IPR007722	mRNA decapping protein 2, Box A domain	Domain
C, D	IPR044099	mRNA decapping enzyme 2 , NUDIX hydrolase domain	Domain
C, D	IPR000086	NUDIX hydrolase domain	Domain
C, D	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
C, D	IPR020084	NUDIX hydrolase, conserved site	Conserved Site
A, B	IPR039900	Pat1-like	Family
A, B	IPR019167	mRNA decay factor PAT1 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.