Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6
Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxyl...
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| Veröffentlicht in: | Journal of molecular biology 2010-08, Vol.401 (2), p.211-222 |
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| creator | Mantri, Monica Krojer, Tobias Bagg, Eleanor A. Webby, Celia J. Butler, Danica S. Kochan, Grazyna Kavanagh, Kathryn L. Oppermann, Udo McDonough, Michael A. Schofield, Christopher J. |
| description | Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine–serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than Nɛ-demethylation, as for analogous enzymes. |
| doi_str_mv | 10.1016/j.jmb.2010.05.054 |
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More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine–serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than Nɛ-demethylation, as for analogous enzymes.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2010.05.054</identifier><identifier>PMID: 20684070</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; Amino Acid Substitution ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; demethylase ; DNA Primers - genetics ; Ehlers–Danlos syndrome type VI ; histone modification ; Humans ; hydroxylase ; In Vitro Techniques ; Iron - metabolism ; Jumonji Domain-Containing Histone Demethylases - chemistry ; Jumonji Domain-Containing Histone Demethylases - genetics ; Jumonji Domain-Containing Histone Demethylases - metabolism ; Ketoglutaric Acids - metabolism ; lysyl hydroxylase ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutant Proteins - chemistry ; Mutant Proteins - genetics ; Mutant Proteins - metabolism ; Nickel - metabolism ; Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - chemistry ; Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - genetics ; Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - metabolism ; Protein Folding ; Recombinant Proteins - chemistry ; Recombinant Proteins - genetics ; Recombinant Proteins - metabolism ; Sequence Homology, Amino Acid ; Static Electricity</subject><ispartof>Journal of molecular biology, 2010-08, Vol.401 (2), p.211-222</ispartof><rights>2010 Elsevier Ltd</rights><rights>Copyright (c) 2010 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c366t-69dac6347bce082e2fe53fe229d00ab83038898a5800bd8ea45f8f257d6b59a63</citedby><cites>FETCH-LOGICAL-c366t-69dac6347bce082e2fe53fe229d00ab83038898a5800bd8ea45f8f257d6b59a63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jmb.2010.05.054$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20684070$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mantri, Monica</creatorcontrib><creatorcontrib>Krojer, Tobias</creatorcontrib><creatorcontrib>Bagg, Eleanor A.</creatorcontrib><creatorcontrib>Webby, Celia J.</creatorcontrib><creatorcontrib>Butler, Danica S.</creatorcontrib><creatorcontrib>Kochan, Grazyna</creatorcontrib><creatorcontrib>Kavanagh, Kathryn L.</creatorcontrib><creatorcontrib>Oppermann, Udo</creatorcontrib><creatorcontrib>McDonough, Michael A.</creatorcontrib><creatorcontrib>Schofield, Christopher J.</creatorcontrib><title>Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine–serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than Nɛ-demethylation, as for analogous enzymes.</description><subject>Amino Acid Sequence</subject><subject>Amino Acid Substitution</subject><subject>Base Sequence</subject><subject>Catalytic Domain</subject><subject>Crystallography, X-Ray</subject><subject>demethylase</subject><subject>DNA Primers - genetics</subject><subject>Ehlers–Danlos syndrome type VI</subject><subject>histone modification</subject><subject>Humans</subject><subject>hydroxylase</subject><subject>In Vitro Techniques</subject><subject>Iron - metabolism</subject><subject>Jumonji Domain-Containing Histone Demethylases - chemistry</subject><subject>Jumonji Domain-Containing Histone Demethylases - genetics</subject><subject>Jumonji Domain-Containing Histone Demethylases - metabolism</subject><subject>Ketoglutaric Acids - metabolism</subject><subject>lysyl hydroxylase</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Mutagenesis, Site-Directed</subject><subject>Mutant Proteins - chemistry</subject><subject>Mutant Proteins - genetics</subject><subject>Mutant Proteins - metabolism</subject><subject>Nickel - metabolism</subject><subject>Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - chemistry</subject><subject>Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - genetics</subject><subject>Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - metabolism</subject><subject>Protein Folding</subject><subject>Recombinant Proteins - chemistry</subject><subject>Recombinant Proteins - genetics</subject><subject>Recombinant Proteins - metabolism</subject><subject>Sequence Homology, Amino Acid</subject><subject>Static Electricity</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE1P3DAURS3UCgboD-gGeVdYZPpsx44jVtXwNWgQC8racuyXklEmGWynIv-ejIZ2iXSlpyedexeHkO8M5gyY-rmerzfVnMP0g5ySH5AZA11mWgn9hcwAOM-4FuqIHMe4BgApcn1IjjgonUMBM_K8CGNMtqVPKQwuDQFpX9P0gpRnj2_9n3ZINtiEGbWdpzd4vlxeZFe4xc5jl-hqjGNL70Yf-rextRHp_cP9lTolX2vbRvz2cU_I883178Vdtnq8XS5-rTInlEqZKr11SuRF5RA0R16jFDVyXnoAW2kBQutSW6kBKq_R5rLWNZeFV5UsrRIn5Md-dxv61wFjMpsmOmxb22E_RFPkulSqkDvy_FOSaa6YVIqJCWV71IU-xoC12YZmY8NoGJidd7M2k3ez825ATsmnztnH_FBt0P9v_BM9AZd7ACcdfxsMJroGO4e-CeiS8X3zyfw7ihKRCQ</recordid><startdate>20100813</startdate><enddate>20100813</enddate><creator>Mantri, Monica</creator><creator>Krojer, Tobias</creator><creator>Bagg, Eleanor A.</creator><creator>Webby, Celia J.</creator><creator>Butler, Danica S.</creator><creator>Kochan, Grazyna</creator><creator>Kavanagh, Kathryn L.</creator><creator>Oppermann, Udo</creator><creator>McDonough, Michael A.</creator><creator>Schofield, Christopher J.</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20100813</creationdate><title>Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6</title><author>Mantri, Monica ; Krojer, Tobias ; Bagg, Eleanor A. ; Webby, Celia J. ; Butler, Danica S. ; Kochan, Grazyna ; Kavanagh, Kathryn L. ; Oppermann, Udo ; McDonough, Michael A. ; Schofield, Christopher J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c366t-69dac6347bce082e2fe53fe229d00ab83038898a5800bd8ea45f8f257d6b59a63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Amino Acid Sequence</topic><topic>Amino Acid Substitution</topic><topic>Base Sequence</topic><topic>Catalytic Domain</topic><topic>Crystallography, X-Ray</topic><topic>demethylase</topic><topic>DNA Primers - genetics</topic><topic>Ehlers–Danlos syndrome type VI</topic><topic>histone modification</topic><topic>Humans</topic><topic>hydroxylase</topic><topic>In Vitro Techniques</topic><topic>Iron - metabolism</topic><topic>Jumonji Domain-Containing Histone Demethylases - chemistry</topic><topic>Jumonji Domain-Containing Histone Demethylases - genetics</topic><topic>Jumonji Domain-Containing Histone Demethylases - metabolism</topic><topic>Ketoglutaric Acids - metabolism</topic><topic>lysyl hydroxylase</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Mutagenesis, Site-Directed</topic><topic>Mutant Proteins - chemistry</topic><topic>Mutant Proteins - genetics</topic><topic>Mutant Proteins - metabolism</topic><topic>Nickel - metabolism</topic><topic>Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - chemistry</topic><topic>Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - genetics</topic><topic>Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - metabolism</topic><topic>Protein Folding</topic><topic>Recombinant Proteins - chemistry</topic><topic>Recombinant Proteins - genetics</topic><topic>Recombinant Proteins - metabolism</topic><topic>Sequence Homology, Amino Acid</topic><topic>Static Electricity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mantri, Monica</creatorcontrib><creatorcontrib>Krojer, Tobias</creatorcontrib><creatorcontrib>Bagg, Eleanor A.</creatorcontrib><creatorcontrib>Webby, Celia J.</creatorcontrib><creatorcontrib>Butler, Danica S.</creatorcontrib><creatorcontrib>Kochan, Grazyna</creatorcontrib><creatorcontrib>Kavanagh, Kathryn L.</creatorcontrib><creatorcontrib>Oppermann, Udo</creatorcontrib><creatorcontrib>McDonough, Michael A.</creatorcontrib><creatorcontrib>Schofield, Christopher J.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mantri, Monica</au><au>Krojer, Tobias</au><au>Bagg, Eleanor A.</au><au>Webby, Celia J.</au><au>Butler, Danica S.</au><au>Kochan, Grazyna</au><au>Kavanagh, Kathryn L.</au><au>Oppermann, Udo</au><au>McDonough, Michael A.</au><au>Schofield, Christopher J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2010-08-13</date><risdate>2010</risdate><volume>401</volume><issue>2</issue><spage>211</spage><epage>222</epage><pages>211-222</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine–serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than Nɛ-demethylation, as for analogous enzymes.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>20684070</pmid><doi>10.1016/j.jmb.2010.05.054</doi><tpages>12</tpages></addata></record> |
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| subjects | Amino Acid Sequence Amino Acid Substitution Base Sequence Catalytic Domain Crystallography, X-Ray demethylase DNA Primers - genetics Ehlers–Danlos syndrome type VI histone modification Humans hydroxylase In Vitro Techniques Iron - metabolism Jumonji Domain-Containing Histone Demethylases - chemistry Jumonji Domain-Containing Histone Demethylases - genetics Jumonji Domain-Containing Histone Demethylases - metabolism Ketoglutaric Acids - metabolism lysyl hydroxylase Models, Molecular Molecular Sequence Data Mutagenesis, Site-Directed Mutant Proteins - chemistry Mutant Proteins - genetics Mutant Proteins - metabolism Nickel - metabolism Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - chemistry Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - genetics Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase - metabolism Protein Folding Recombinant Proteins - chemistry Recombinant Proteins - genetics Recombinant Proteins - metabolism Sequence Homology, Amino Acid Static Electricity |
| title | Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6 |
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