{"entry": {"accession": "MF7000824", "general": {"name": "Human Dcps", "pdb_id": "1xml", "exp_method": "X-ray", "resolution": "2.00", "assembly": "Homodimer", "source_organism": "Homo sapiens", "publication": {"pmid": "15769464", "authors": "Chen N, Walsh MA, Liu Y, Parker R, Song H", "title": "Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping.", "journal": "J. Mol. Biol.", "year": "2005", "issue": "4", "volume": "347", "pages": "707-18", "abstract": "Eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 3'-5' mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids. We report the structures of DcpS in ligand-free form and in a complex with m7GDP. apo-DcpS is a symmetric dimer, strikingly different from the asymmetric dimer observed in the structures of DcpS with bound cap analogues. In contrast, and similar to the m7GpppG-DcpS complex, DcpS with bound m7GDP is an asymmetric dimer in which the closed state appears to be the substrate-bound complex, whereas the open state mimics the product-bound complex. Comparisons of these structures revealed conformational changes of both the N-terminal swapped-dimeric domain and the cap-binding pocket upon cap binding. Moreover, Tyr273 in the cap-binding pocket displays remarkable conformational changes upon cap binding. Mutagenesis and biochemical analysis suggest that Tyr273 seems to play an important role in cap binding and product release. Examination of the crystallographic B-factors indicates that the N-terminal domain in apo-DcpS is inherently flexible, and in a dynamic state ready for substrate binding and product release."}}, "function": {"molecular_function": {"go": [{"accession": "GO:0140932", "name": "5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity"}, {"accession": "GO:0042802", "name": "identical protein binding"}, {"accession": "GO:0000340", "name": "RNA 7-methylguanosine cap binding"}, {"accession": "GO:0004532", "name": "RNA exonuclease activity"}]}, "cellular_component": {"go": [{"accession": "GO:0005737", "name": "cytoplasm"}, {"accession": "GO:0005829", "name": "cytosol"}, {"accession": "GO:0005739", "name": "mitochondrion"}, {"accession": "GO:0005654", "name": "nucleoplasm"}, {"accession": "GO:0005634", "name": "nucleus"}, {"accession": "GO:0000932", "name": "P-body"}]}, "biological_process": {"go": [{"accession": "GO:0000290", "name": "deadenylation-dependent decapping of nuclear-transcribed mRNA"}, {"accession": "GO:0045292", "name": "mRNA cis splicing, via spliceosome"}, {"accession": "GO:0110156", "name": "mRNA methylguanosine-cap decapping"}, {"accession": "GO:0000288", "name": "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay"}]}}, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "m7GpppX diphosphatase", "source_organism": "Homo sapiens", "uniprot": {"id": "Q96C86", "start": "38", "end": "336", "coverage": "88%", "sequence": "MADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS", "length": "337"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "95", "region_end": "105"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "126", "region_end": "130"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "141", "region_end": "149"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "159", "region_end": "166"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "166", "region_end": "174"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "178", "region_end": "186"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "190", "region_end": "194"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "217", "region_end": "220"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "234", "region_end": "238"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "239", "region_end": "241"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "242", "region_end": "262"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "264", "region_end": "266"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "303", "region_end": "313"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "315", "region_end": "320"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "330", "region_end": "341"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "53", "region_end": "61"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "66", "region_end": "72"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "84", "region_end": "91"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "108", "region_end": "115"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "118", "region_end": "124"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "132", "region_end": "137"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "153", "region_end": "158"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "196", "region_end": "198"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "205", "region_end": "209"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "222", "region_end": "227"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "268", "region_end": "273"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "282", "region_end": "287"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "300", "region_end": "302"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "322", "region_end": "327"}, {"region_type": "pfam", "region_id": "PF11969", "region_name": "Scavenger mRNA decapping enzyme C-term binding", "region_start": "174", "region_end": "292"}]}}, {"id": "B", "name": "m7GpppX diphosphatase", "source_organism": "Homo sapiens", "uniprot": {"id": "Q96C86", "start": "40", "end": "336", "coverage": "88%", "sequence": "MADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS", "length": "337"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "95", "region_end": "105"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "126", "region_end": "130"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "141", "region_end": "149"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "159", "region_end": "166"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "166", "region_end": "174"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "178", "region_end": "186"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "190", "region_end": "194"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "217", "region_end": "220"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "234", "region_end": "238"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "239", "region_end": "241"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "242", "region_end": "262"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "264", "region_end": "266"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "303", "region_end": "313"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "315", "region_end": "320"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "330", "region_end": "340"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "53", "region_end": "61"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "66", "region_end": "72"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "84", "region_end": "91"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "109", "region_end": "115"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "118", "region_end": "123"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "132", "region_end": "137"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "153", "region_end": "158"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "196", "region_end": "198"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "205", "region_end": "209"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "222", "region_end": "227"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "268", "region_end": "273"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "282", "region_end": "287"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "300", "region_end": "302"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "322", "region_end": "327"}, {"region_type": "pfam", "region_id": "PF11969", "region_name": "Scavenger mRNA decapping enzyme C-term binding", "region_start": "174", "region_end": "292"}]}}]}, "evidence": {"evidence_level": "Indirect evidence", "evidence_coverage": "Only some parts of the structure participates in mutual synergistic folding.", "sequence_domain": "Scavenger mRNA decapping enzyme (DcpS)", "complex_evidence": "Multidomain structure, where the domain-swapped N-terminal domain is responsible for dimerization. The extensive interface, symmetry, topology, beta sheet augmentation and buried surface area suggest that the N-terminal dimerization domain behaves as a single rigid domain and the monomers would not be stable on their own. Gel-filtration chromatography also suggested a dimeric form (PMID:15068804).", "chain_evidence": [{"chain_id": "B", "support": "N/A"}, {"chain_id": "A", "support": "N/A"}]}, "related_structures": {"id": ["MF7000822", "MF7000823", "MF7000824", "MF7000825", "MF7000826", "MF7000827", "MF7000828", "MF7000829"]}}}