| Entry | Database: PDB / ID: 6trq |
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| Title | S.c. Scavenger Decapping Enzyme DcpS in complex with the capped RNA dinucleotide m7G-GU |
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Components | - Capped RNA dinucleotide
- m7GpppX diphosphatase
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Keywords | HYDROLASE / mRNA decapping / mRNA degradation / decapping |
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| Function / homology | Function and homology information
exoribonuclease activator activity / m7G(5')pppN diphosphatase complex / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / mRNA decay by 3' to 5' exoribonuclease / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / RNA 7-methylguanosine cap binding / response to osmotic stress ...exoribonuclease activator activity / m7G(5')pppN diphosphatase complex / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / mRNA decay by 3' to 5' exoribonuclease / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / RNA 7-methylguanosine cap binding / response to osmotic stress / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / response to nutrient / cellular response to starvation / P-body / response to heat / response to oxidative stress / protein heterodimerization activity / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / identical protein binding / nucleus / cytoplasmSimilarity search - Function Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like superfamilySimilarity search - Domain/homology |
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| Biological species |  Saccharomyces cerevisiae S288C (yeast) synthetic construct (others) |
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| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.944 Å |
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Authors | Fuchs, A.-L. / Neu, A. / Sprangers, R. |
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| Funding support | Germany, 2items | Organization | Grant number | Country |
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| European Research Council | 616052 | Germany | | German Research Foundation | SFB 960/2, B12 | Germany |
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Molecular basis of the selective processing of short mRNA substrates by the DcpS mRNA decapping enzyme. Authors: Fuchs, A.L. / Wurm, J.P. / Neu, A. / Sprangers, R. |
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| History | | Deposition | Dec 19, 2019 | Deposition site: PDBE / Processing site: PDBE |
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| Revision 1.0 | Jul 22, 2020 | Provider: repository / Type: Initial release |
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| Revision 1.1 | Aug 12, 2020 | Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id |
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| Revision 1.2 | Aug 26, 2020 | Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last |
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| Revision 1.3 | Jan 24, 2024 | Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id |
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| Revision 2.0 | Mar 6, 2024 | Group: Atomic model / Data collection ...Atomic model / Data collection / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight |
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| Revision 2.1 | Oct 1, 2025 | Group: Advisory / Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn Item: _pdbx_entry_details.has_protein_modification |
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| Revision 3.0 | Dec 17, 2025 | Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_PDB_caveat.text / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id |
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