2LYD | pdb_00002lyd

The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	KOG2045_5th	e2lydB1	A: extended segments	X: DCP1-binding motif (From Topology)	H: DCP1-binding motif (From Topology)	T: DCP1-binding motif	F: KOG2045_5th	ECOD (1.6)
A	DCP1	e2lydA1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: DCP1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF18245	5-3 exonuclease XRN1 DCP1-binding motif (XRN1_DBM)	5-3 exonuclease XRN1 DCP1-binding motif	-	Motif
A	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	Pacman protein	5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding 5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule 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 nuclear-transcribed mRNA catabolic process, non-stop decay developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation multicellular organismal process imaginal disc morphogenesis animal organ development instar larval or pupal development metamorphosis multicellular organism development anatomical structure morphogenesis instar larval or pupal morphogenesis imaginal disc development imaginal disc fusion, thorax closure post-embryonic animal morphogenesis anatomical structure development imaginal disc fusion post-embryonic development animal organ morphogenesis post-transcriptional regulation of gene expression regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing post-transcriptional gene silencing negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death appendage development post-embryonic appendage morphogenesis wing disc development imaginal disc-derived wing morphogenesis imaginal disc-derived appendage morphogenesis wing disc morphogenesis appendage morphogenesis imaginal disc-derived appendage development morphogenesis of embryonic epithelium epithelium development embryonic morphogenesis morphogenesis of an epithelium embryo development tissue development dorsal closure embryonic development via the syncytial blastoderm tissue morphogenesis embryo development ending in birth or egg hatching wound healing response to stimulus response to stress response to wounding regulation of growth regulation of developmental growth regulation of developmental process regulation of imaginal disc growth developmental growth growth positive regulation of biological process positive regulation of developmental process positive regulation of growth imaginal disc growth positive regulation of imaginal disc growth positive regulation of developmental growth rRNA catabolic process rRNA metabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay regulation of cellular component organization organelle assembly regulation of cytoplasmic mRNA processing body assembly P-body assembly membraneless organelle assembly regulation of cellular component biogenesis regulation of organelle organization cellular component biogenesis cellular component organization organelle organization cellular component assembly regulation of organelle assembly cellular component organization or biogenesis	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex P-body intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A	Decapping protein 1	RNA binding binding nucleic acid binding mRNA binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein 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 nucleobase-containing compound metabolic process 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 deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing post-transcriptional gene silencing multicellular organismal process blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo cellular process involved in reproduction in multicellular organism female gamete generation pole plasm oskar mRNA localization oocyte development cellular component biogenesis multicellular organism development localization cellular component assembly cell differentiation anatomical structure development cell maturation RNA localization pole plasm mRNA localization developmental process pole plasm RNA localization embryonic pattern specification oocyte anterior/posterior axis specification cytoplasm organization developmental maturation anatomical structure maturation maternal determination of anterior/posterior axis, embryo germ cell development intracellular mRNA localization involved in anterior/posterior axis specification axis specification sexual reproduction cellular developmental process reproductive process segmentation pattern specification process cell development developmental process involved in reproduction embryo development gamete generation tripartite regional subdivision cellular component organization embryonic axis specification anterior/posterior axis specification cellular component organization or biogenesis oocyte axis specification oocyte construction intracellular mRNA localization multicellular organismal reproductive process oogenesis regionalization pole plasm assembly intracellular mRNA localization involved in pattern specification process macromolecule localization oocyte differentiation regulation of cellular component organization organelle assembly regulation of cytoplasmic mRNA processing body assembly P-body assembly membraneless organelle assembly regulation of cellular component biogenesis regulation of organelle organization organelle organization regulation of organelle assembly	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016494	5'-3' exoribonuclease 1	Family
B	IPR040992	5'-3' exoribonuclease 1, D1 domain	Domain
B	IPR047007	5'-3' exoribonuclease 1, D1 domain superfamily	Homologous Superfamily
B	IPR047008	5'-3' exoribonuclease 1, SH3-like domain superfamily	Homologous Superfamily
B	IPR027073	5'-3' exoribonuclease	Family
B	IPR040587	5-3 exonuclease XRN1, DCP1-binding motif	Domain
B	IPR041106	Exoribonuclease Xrn1, D2/D3 domain	Domain
B	IPR041385	5'-3' exoribonuclease 1, SH3-like domain	Domain
B	IPR041412	Xrn1, helical domain	Domain
B	IPR004859	Xrn1, N-terminal	Domain
A	IPR010334	mRNA-decapping enzyme subunit 1	Family
A	IPR031953	mRNA-decapping enzyme, C-terminal	Domain
A	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.