1VLR | pdb_00001vlr

Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution

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)
B	d1vlrb1	Alpha and beta proteins (a+b)	HIT-like	HIT-like	mRNA decapping enzyme DcpS C-terminal domain	mRNA decapping enzyme DcpS C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1vlrb2	Alpha and beta proteins (a+b)	mRNA decapping enzyme DcpS N-terminal domain	mRNA decapping enzyme DcpS N-terminal domain	mRNA decapping enzyme DcpS N-terminal domain	mRNA decapping enzyme DcpS N-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1vlra1	Alpha and beta proteins (a+b)	HIT-like	HIT-like	mRNA decapping enzyme DcpS C-terminal domain	mRNA decapping enzyme DcpS C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1vlra2	Alpha and beta proteins (a+b)	mRNA decapping enzyme DcpS N-terminal domain	mRNA decapping enzyme DcpS N-terminal domain	mRNA decapping enzyme DcpS N-terminal domain	mRNA decapping enzyme DcpS N-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	DcpS C-terminal domain-like	8029125	4001251	SCOP2 (2022-06-29)
B	SCOP2 Family	mRNA decapping enzyme DcpS N-terminal domain	8029127	4001353	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	HIT-like	8041504	3000223	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	mRNA decapping enzyme DcpS N-terminal domain	8041506	3001367	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	mRNA decapping enzyme DcpS N-terminal domain	8041506	3001367	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HIT-like	8041504	3000223	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		e1vlrB1	A: Hypothetical protein TM0160	X: Hypothetical protein TM0160	H: Hypothetical protein TM0160	T:	F:	ECOD (20:10:01)
B		e1vlrB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)
A		e1vlrA1	A: Hypothetical protein TM0160	X: Hypothetical protein TM0160	H: Hypothetical protein TM0160	T:	F:	ECOD (20:10:01)
A		e1vlrA2	A: HIT-like	X: HIT-related	H: HIT-related	T: DcpS_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.200.40	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	3.30.2240.10	Alpha Beta	2-Layer Sandwich	mRNA decapping enzyme DcpS N-terminal fold	mRNA decapping enzyme DcpS N-terminal domain	CATH (4.3.0)
B	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
A	3.30.200.40	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	3.30.2240.10	Alpha Beta	2-Layer Sandwich	mRNA decapping enzyme DcpS N-terminal fold	mRNA decapping enzyme DcpS N-terminal domain	CATH (4.3.0)
A	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11969	Scavenger mRNA decapping enzyme C-term binding (DcpS_C)	Scavenger mRNA decapping enzyme C-term binding	-	Family
A, B	PF05652	Scavenger mRNA decapping enzyme (DcpS) N-terminal (DcpS)	Scavenger mRNA decapping enzyme (DcpS) N-terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	mRNA decapping enzyme	RNA binding binding RNA 7-methylguanosine cap binding nucleic acid binding RNA cap binding pyrophosphatase activity 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity identical protein binding protein 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 RNA splicing nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex P-body nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011145	Scavenger mRNA decapping enzyme, N-terminal	Homologous Superfamily
A, B	IPR008594	Scavenger mRNA decapping enzyme DcpS/DCS2	Family
A, B	IPR036265	HIT-like superfamily	Homologous Superfamily
A, B	IPR019808	Histidine triad, conserved site	Conserved Site

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.