2QKM | pdb_00002qkm

The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex

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)
H	d2qkmh1	All alpha proteins	Dcp2 domain-like	Dcp2 domain-like	Dcp2 box A domain	mRNA decapping enzyme Dcp2p, N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
H	d2qkmh2	Alpha and beta proteins (a+b)	Nudix	Nudix	mRNA decapping enzyme-like	automated matches	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
D	d2qkmd1	All alpha proteins	Dcp2 domain-like	Dcp2 domain-like	Dcp2 box A domain	mRNA decapping enzyme Dcp2p, N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
D	d2qkmd2	Alpha and beta proteins (a+b)	Nudix	Nudix	mRNA decapping enzyme-like	automated matches	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Dcp2 domain-like	8036072	3001348	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Dcp2 domain-like	8036072	3001348	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nudix	8036684	3000098	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Dcp2 domain-like	8036072	3001348	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8036684	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Dcp2 domain-like	8036072	3001348	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)
H		e2qkmH5	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: V-set	F:	ECOD (20:10:01)
F		e2qkmF3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: V-set	F:	ECOD (20:10:01)
D		e2qkmD1	A: HTH	X: HTH	H: winged helix domain	T: Plexin_RBD	F:	ECOD (20:10:01)
B		e2qkmB3	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: V-set	F:	ECOD (20:10:01)
G		e2qkmG1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: TetR_N	F:	ECOD (20:10:01)
E		e2qkmE1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: TetR_N	F:	ECOD (20:10:01)
C		e2qkmC1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: TetR_N	F:	ECOD (20:10:01)
A		e2qkmA1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: TetR_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.10.1050	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Dcp2, box A domain	CATH (4.3.0)
H	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
F	1.10.10.1050	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Dcp2, box A domain	CATH (4.3.0)
F	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
D	1.10.10.1050	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Dcp2, box A domain	CATH (4.3.0)
D	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
B	1.10.10.1050	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Dcp2, box A domain	CATH (4.3.0)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
G	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
E	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
C	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain
B, D, F, H	PF05026	Dcp2, box A domain (DCP2)	Dcp2, box A domain	This domain is always found to the amino terminal side of Pfam:PF00293. This domain is specific to mRNA decapping protein 2 and this region has been termed Box A [2]. Removal of the cap structure is catalysed by the Dcp1-Dcp2 complex [3].	Domain
A, C, E, G	PF06058	Dcp1-like decapping family (DCP1)	Dcp1-like decapping family	An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (Pfam:PF05026). The precise role of these proteins in the decapping reaction have not been es ...	An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (Pfam:PF05026). The precise role of these proteins in the decapping reaction have not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	SPAC19A8.12 protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding RNA binding mRNA cap binding nucleic acid binding RNA cap binding mRNA binding manganese ion binding transition metal ion binding single-stranded RNA 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 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	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 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 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 cytosol protein-containing complex RNA decapping complex 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 cytosol protein-containing complex RNA decapping complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, C, E, G	SPBC3B9.21 protein	enzyme regulator activity enzyme activator activity mRNA phosphatase activator activity molecular function activator activity molecular function regulator activity RNA binding binding nucleic acid binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process 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 regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process 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 primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of primary 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 positive regulation of mRNA metabolic process positive regulation of RNA metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process mRNA methylguanosine-cap decapping positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 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 cytosol protein-containing complex RNA decapping complex 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 cytosol protein-containing complex RNA decapping complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR036189	mRNA decapping protein 2, Box A domain superfamily	Homologous Superfamily
B, D, F, H	IPR007722	mRNA decapping protein 2, Box A domain	Domain
B, D, F, H	IPR044099	mRNA decapping enzyme 2 , NUDIX hydrolase domain	Domain
B, D, F, H	IPR000086	NUDIX hydrolase domain	Domain
B, D, F, H	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR020084	NUDIX hydrolase, conserved site	Conserved Site
A, C, E, G	IPR010334	mRNA-decapping enzyme subunit 1	Family
A, C, E, G	IPR011993	PH-like domain superfamily	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.