{"@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/1360011145773536768.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1186/1472-6807-11-13"}},{"identifier":{"@type":"URI","@value":"https://link.springer.com/content/pdf/10.1186/1472-6807-11-13.pdf"}}],"dc:title":[{"@value":"Structural analysis of heme proteins: implications for design and prediction"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Heme is an essential molecule and plays vital roles in many biological processes. The structural determination of a large number of heme proteins has made it possible to study the detailed chemical and structural properties of heme binding environment. Knowledge of these characteristics can provide valuable guidelines in the design of novel heme proteins and help us predict unknown heme binding proteins.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>In this paper, we constructed a non-redundant dataset of 125 heme-binding protein chains and found that these heme proteins encompass at least 31 different structural folds with all-α class as the dominating scaffold. Heme binding pockets are enriched in aromatic and non-polar amino acids with fewer charged residues. The differences between apo and holo forms of heme proteins in terms of the structure and the binding pockets have been investigated. In most cases the proteins undergo small conformational changes upon heme binding. We also examined the CP (cysteine-proline) heme regulatory motifs and demonstrated that the conserved dipeptide has structural implications in protein-heme interactions.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions</jats:title>\n            <jats:p>Our analysis revealed that heme binding pockets show special features and that most of the heme proteins undergo small conformational changes after heme binding, suggesting the apo structures can be used for structure-based heme protein prediction and as scaffolds for future heme protein design.</jats:p>\n          </jats:sec>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380011145773536769","@type":"Researcher","foaf:name":[{"@value":"Ting Li"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011145773536768","@type":"Researcher","foaf:name":[{"@value":"Herbert L Bonkovsky"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011145773536770","@type":"Researcher","foaf:name":[{"@value":"Jun-tao Guo"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"14726807"}],"prism:publicationName":[{"@value":"BMC Structural Biology"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2011-03-03","prism:volume":"11","prism:number":"1","prism:startingPage":"13"},"reviewed":"false","url":[{"@id":"https://link.springer.com/content/pdf/10.1186/1472-6807-11-13.pdf"}],"createdAt":"2011-03-03","modifiedAt":"2021-09-01","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050002213722134272","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme"},{"@value":"Control of seed dormancy and germination by DOG1‐AHG1 PP2C phosphatase complex via binding to heme"}]},{"@id":"https://cir.nii.ac.jp/crid/1050292936859987840","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Repressor activity of SqrR, a master regulator of persulfide-responsive genes, is regulated by heme coordination"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013171679273344","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Global analysis of heme proteins elucidates the correlation between heme distortion and heme-binding pocket"}]},{"@id":"https://cir.nii.ac.jp/crid/1360022307169917312","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin"}]},{"@id":"https://cir.nii.ac.jp/crid/1360290617665249408","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1360294643822326656","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of Enzymes from <i>Pseudogluconobacter saccharoketogenes</i> Producing <scp>d</scp>-Glucaric Acid from <scp>d</scp>-Glucose"}]},{"@id":"https://cir.nii.ac.jp/crid/1360298345423231232","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network"}]},{"@id":"https://cir.nii.ac.jp/crid/1360576118831749632","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Heme‐dependent recognition of 5‐aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX"}]},{"@id":"https://cir.nii.ac.jp/crid/1360857593747826816","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Dissection and Reconstitution Provide Insights into Electron Transport in the Membrane-Bound Aldehyde Dehydrogenase Complex of Gluconacetobacter diazotrophicus"}]},{"@id":"https://cir.nii.ac.jp/crid/2050870367089697408","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Structure of heme-binding pocket in heme protein is generally rigid and can be predicted by 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