{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360004233530361600.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1038/srep13836"}},{"identifier":{"@type":"URI","@value":"https://www.nature.com/articles/srep13836"}},{"identifier":{"@type":"URI","@value":"https://www.nature.com/articles/srep13836.pdf"}},{"identifier":{"@type":"PMID","@value":"26370172"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title><jats:p>Alkaline D-peptidase from <jats:italic>Bacillus cereus</jats:italic> DF4-B, called ADP, is a D-stereospecific endopeptidase reacting with oligopeptides containing D-phenylalanine (D-Phe) at N-terminal penultimate residue. ADP has attracted increasing attention because it is useful as a catalyst for synthesis of D-Phe oligopeptides or, with the help of substrate mimetics, L-amino acid peptides and proteins. Structure and functional analysis of ADP is expected to elucidate molecular mechanism of ADP. In this study, the crystal structure of ADP (apo) form was determined at 2.1 Å resolution. The fold of ADP is similar to that of the class C penicillin-binding proteins of type-AmpH. Docking simulations and fragment molecular orbital analyses of two peptides, (D-Phe)<jats:sub>4</jats:sub> and (D-Phe)<jats:sub>2</jats:sub>-(L-Phe)<jats:sub>2</jats:sub>, with the putative substrate binding sites of ADP indicated that the P<jats:sub>1</jats:sub> residue of the peptide interacts with hydrophobic residues at the S<jats:sub>1</jats:sub> site of ADP. Furthermore, molecular dynamics simulation of ADP for 50 nsec suggested that the ADP forms large cavity at the active site. Formation of the cavity suggested that the ADP has open state in the solution. For the ADP, having the open state is convenient to bind the peptides having bulky side chain, such as (D-Phe)<jats:sub>4</jats:sub>. Taken together, we predicted peptide recognition mechanism of ADP.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1420845751144431616","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"80748541"},{"@type":"NRID","@value":"1000080748541"},{"@type":"NRID","@value":"9000239878853"},{"@type":"NRID","@value":"9000410186151"},{"@type":"NRID","@value":"9000413332357"},{"@type":"NRID","@value":"9000413498229"},{"@type":"NRID","@value":"9000267809759"},{"@type":"NRID","@value":"9000241681519"},{"@type":"NRID","@value":"9000414945633"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/sn-k21-tLs"}],"foaf:name":[{"@value":"Shogo Nakano"}]},{"@id":"https://cir.nii.ac.jp/crid/1380004233530361861","@type":"Researcher","foaf:name":[{"@value":"Seiji Okazaki"}]},{"@id":"https://cir.nii.ac.jp/crid/1380004233530361732","@type":"Researcher","foaf:name":[{"@value":"Erika Ishitsubo"}]},{"@id":"https://cir.nii.ac.jp/crid/1380004233530361612","@type":"Researcher","foaf:name":[{"@value":"Nobuhiro Kawahara"}]},{"@id":"https://cir.nii.ac.jp/crid/1380004233530361604","@type":"Researcher","foaf:name":[{"@value":"Hidenobu Komeda"}]},{"@id":"https://cir.nii.ac.jp/crid/1030285133371383552","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"10221433"},{"@type":"NRID","@value":"1000010221433"},{"@type":"NRID","@value":"9000019963939"},{"@type":"NRID","@value":"9000021230865"},{"@type":"NRID","@value":"9000021764865"},{"@type":"NRID","@value":"9000303995803"},{"@type":"NRID","@value":"9000020080899"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/read0173591"}],"foaf:name":[{"@value":"Hiroaki Tokiwa"}]},{"@id":"https://cir.nii.ac.jp/crid/1420282801203645312","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"00222589"},{"@type":"NRID","@value":"1000000222589"},{"@type":"NRID","@value":"9000288542203"},{"@type":"NRID","@value":"9000309180002"},{"@type":"NRID","@value":"9000413750892"},{"@type":"NRID","@value":"9000412290977"},{"@type":"NRID","@value":"9000004123654"},{"@type":"NRID","@value":"9000256921539"},{"@type":"NRID","@value":"9000256026052"},{"@type":"NRID","@value":"9000001262351"},{"@type":"NRID","@value":"9000002547778"},{"@type":"NRID","@value":"9000021905771"},{"@type":"NRID","@value":"9000363290721"},{"@type":"NRID","@value":"9000401542869"},{"@type":"NRID","@value":"9000401955914"},{"@type":"NRID","@value":"9000238234587"},{"@type":"NRID","@value":"9000004160110"},{"@type":"NRID","@value":"9000363291940"},{"@type":"NRID","@value":"9000309558310"},{"@type":"NRID","@value":"9000303638774"},{"@type":"NRID","@value":"9000401532898"},{"@type":"NRID","@value":"9000402386703"},{"@type":"NRID","@value":"9000363289003"},{"@type":"NRID","@value":"9000403836113"},{"@type":"NRID","@value":"9000021895834"},{"@type":"NRID","@value":"9000004196753"},{"@type":"NRID","@value":"9000005262292"},{"@type":"NRID","@value":"9000363290750"},{"@type":"NRID","@value":"9000021011713"},{"@type":"NRID","@value":"9000300227242"},{"@type":"NRID","@value":"9000019243939"},{"@type":"NRID","@value":"9000253146179"},{"@type":"NRID","@value":"9000253175350"},{"@type":"NRID","@value":"9000348294594"},{"@type":"NRID","@value":"9000004574011"},{"@type":"NRID","@value":"9000238411811"},{"@type":"NRID","@value":"9000363290720"},{"@type":"NRID","@value":"9000363290722"},{"@type":"NRID","@value":"9000363170701"},{"@type":"NRID","@value":"9000342803314"},{"@type":"NRID","@value":"9000021905620"},{"@type":"NRID","@value":"9000021812199"},{"@type":"NRID","@value":"9000004500690"},{"@type":"NRID","@value":"9000399001136"},{"@type":"NRID","@value":"9000363305607"},{"@type":"NRID","@value":"9000004164464"},{"@type":"NRID","@value":"9000020323374"},{"@type":"NRID","@value":"9000253152510"},{"@type":"NRID","@value":"9000004258383"},{"@type":"NRID","@value":"9000021905623"},{"@type":"NRID","@value":"9000020720649"},{"@type":"NRID","@value":"9000020847200"},{"@type":"NRID","@value":"9000257180408"},{"@type":"NRID","@value":"9000004258374"},{"@type":"NRID","@value":"9000007039677"},{"@type":"NRID","@value":"9000286636759"},{"@type":"NRID","@value":"9000255961740"},{"@type":"NRID","@value":"9000018472423"},{"@type":"NRID","@value":"9000021038152"},{"@type":"NRID","@value":"9000387906278"},{"@type":"NRID","@value":"9000254596702"},{"@type":"NRID","@value":"9000401960329"},{"@type":"NRID","@value":"9000020991460"},{"@type":"NRID","@value":"9000239878854"},{"@type":"NRID","@value":"9000408798481"},{"@type":"NRID","@value":"9000363293228"},{"@type":"NRID","@value":"9000020744806"},{"@type":"NRID","@value":"9000021027776"},{"@type":"NRID","@value":"9000314073416"},{"@type":"NRID","@value":"9000242755771"},{"@type":"NRID","@value":"9000363297056"},{"@type":"NRID","@value":"9000414945635"},{"@type":"NRID","@value":"9000363277704"},{"@type":"NRID","@value":"9000363277132"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/read0020081"}],"foaf:name":[{"@value":"Yasuhisa Asano"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"20452322"}],"prism:publicationName":[{"@value":"Scientific Reports"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2015-09-15","prism:volume":"5","prism:number":"1","prism:startingPage":"13836"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","dc:rights":["https://creativecommons.org/licenses/by/4.0","https://creativecommons.org/licenses/by/4.0"],"url":[{"@id":"https://www.nature.com/articles/srep13836"},{"@id":"https://www.nature.com/articles/srep13836.pdf"}],"createdAt":"2015-09-15","modifiedAt":"2023-01-05","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Models,%20Molecular","dc:title":"Models, Molecular"},{"@id":"https://cir.nii.ac.jp/all?q=Binding%20Sites","dc:title":"Binding Sites"},{"@id":"https://cir.nii.ac.jp/all?q=Protein%20Conformation","dc:title":"Protein Conformation"},{"@id":"https://cir.nii.ac.jp/all?q=Molecular%20Dynamics%20Simulation","dc:title":"Molecular Dynamics Simulation"},{"@id":"https://cir.nii.ac.jp/all?q=Ligands","dc:title":"Ligands"},{"@id":"https://cir.nii.ac.jp/all?q=Article","dc:title":"Article"},{"@id":"https://cir.nii.ac.jp/all?q=Adenosine%20Diphosphate","dc:title":"Adenosine Diphosphate"},{"@id":"https://cir.nii.ac.jp/all?q=Molecular%20Docking%20Simulation","dc:title":"Molecular Docking Simulation"},{"@id":"https://cir.nii.ac.jp/all?q=Bacillus%20cereus","dc:title":"Bacillus cereus"},{"@id":"https://cir.nii.ac.jp/all?q=Endopeptidases","dc:title":"Endopeptidases"},{"@id":"https://cir.nii.ac.jp/all?q=Penicillin-Binding%20Proteins","dc:title":"Penicillin-Binding Proteins"},{"@id":"https://cir.nii.ac.jp/all?q=Peptides","dc:title":"Peptides"},{"@id":"https://cir.nii.ac.jp/all?q=Protein%20Binding","dc:title":"Protein Binding"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040000782257761792","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"25460157"},{"@type":"JGN","@value":"JP25460157"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25460157/"}],"notation":[{"@language":"ja","@value":"高精度全電子計算に基づく新規創薬手法の開発とその応用"},{"@language":"en","@value":"Development and its Application of Novel Drug Design based on the first-principles calculation"}]},{"@id":"https://cir.nii.ac.jp/crid/1040282257265023232","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"26292041"},{"@type":"JGN","@value":"JP26292041"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26292041/"}],"notation":[{"@language":"ja","@value":"アルドキシムーニトリル経路の酵素類の有機合成への利用と生理学的意義の解明"},{"@language":"en","@value":"Enzymes in the Aldoxime-Nitrile pathway -application to organic synthesis and their physiological importance-"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050306506451698432","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Heterochiral coupling in non-ribosomal peptide macrolactamization"}]},{"@id":"https://cir.nii.ac.jp/crid/1360004233980938624","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011143981808768","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Resistance to ?-lactam antibiotics"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011145417254272","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Crystal Structure and Functional Characterization of a D-Stereospecific Amino Acid Amidase from Ochrobactrum anthropi SV3, a New Member of the Penicillin-recognizing Proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1360025429422363392","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials"}]},{"@id":"https://cir.nii.ac.jp/crid/1360283691648882048","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Comparative Molecular Dynamics Simulation Study of Crystal Environment Effect on Protein Structure"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292619960339328","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fragmentation Methods: A Route to Accurate Calculations on Large 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Rue61a – an insight into catalytic promiscuity"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107368668127872","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Dali server: conservation mapping in 3D"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107370089014528","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Features and development of <i>Coot</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388844066759296","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Reconstructing a Missing Link in the Evolution of a Recently Diverged Phosphotriesterase by Active-Site Loop Remodeling"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388845247830528","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structural Relationship between the Active Sites of β-Lactam-Recognizing and Amidase Signature Enzymes: Convergent Evolution?"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670318219879424","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Synthesis of d-phenylalanine oligopeptides catalyzed by alkaline d-peptidase from Bacillus cereus DF4-B"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951793328804736","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Enzymes Acting on d-Amino Acid Containing Peptides"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951793653974912","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"An Alkaline D-Stereospecific Endopeptidase with β-Lactamase Activity from Bacillus cereus"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951794146494720","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A smooth particle mesh Ewald method"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951794251109760","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"ASEDock-Docking Based on Alpha Spheres and Excluded Volumes"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951795380194688","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fragment molecular orbital calculation using the RI-MP2 method"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269005845888","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Crystal Structures of Covalent Complexes of β-Lactam Antibiotics with <i>Escherichia coli</i> Penicillin-Binding Protein 5: Toward an Understanding of Antibiotic Specificity"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269451938048","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"<i>REFMAC</i>5 for the refinement of macromolecular crystal structures"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269690396928","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-D-alanine."}]},{"@id":"https://cir.nii.ac.jp/crid/1522543655075333248","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Enzymes Acting on Peptides Containing D-Amino Acid"},{"@language":"ja-Kana","@value":"Enzymes Acting on Peptides Containing D Amino Acid"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1038/srep13836"},{"@type":"KAKEN","@value":"PRODUCT-20535905"},{"@type":"KAKEN","@value":"PRODUCT-20655000"},{"@type":"OPENAIRE","@value":"doi_dedup___::32406620bf390225f2143a36737907fa"},{"@type":"CROSSREF","@value":"10.1016/j.cbpa.2024.102465_references_DOI_GgqiOlaCgwMwiGmtwPlpRbpZACI"},{"@type":"CROSSREF","@value":"10.1038/s41929-020-0456-7_references_DOI_GgqiOlaCgwMwiGmtwPlpRbpZACI"},{"@type":"CROSSREF","@value":"10.1021/acs.jcim.8b00649_references_DOI_GgqiOlaCgwMwiGmtwPlpRbpZACI"}]}