The APOBEC-2 crystal structure and functional implications for the deaminase AID
APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA 1 , 2 . Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an AP...
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description | APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA
1
,
2
. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies
3
, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus
4
,
5
,
6
,
7
. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long α-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation. |
doi_str_mv | 10.1038/nature05492 |
format | Article |
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1
,
2
. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies
3
, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus
4
,
5
,
6
,
7
. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long α-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.</description><identifier>ISSN: 0028-0836</identifier><identifier>ISSN: 1476-4687</identifier><identifier>EISSN: 1476-4687</identifier><identifier>EISSN: 1476-4679</identifier><identifier>DOI: 10.1038/nature05492</identifier><identifier>PMID: 17187054</identifier><identifier>CODEN: NATUAS</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>Amino Acid Sequence ; APOBEC Deaminases ; Binding Sites ; Biological and medical sciences ; Crystal structure ; Crystalline structure ; Crystallography, X-Ray ; Cytidine Deaminase - chemistry ; Cytidine Deaminase - genetics ; Cytidine Deaminase - metabolism ; Deamination ; Deoxyribonucleic acid ; Dimerization ; DNA ; DNA - metabolism ; Enzymes ; Fundamental and applied biological sciences. Psychology ; Hepatitis ; Hepatitis B virus ; Human immunodeficiency virus ; Humanities and Social Sciences ; Humans ; Hyper-IgM Immunodeficiency Syndrome - enzymology ; Hyper-IgM Immunodeficiency Syndrome - genetics ; Immunology ; letter ; Models, Molecular ; Molecular biophysics ; Molecular Sequence Data ; multidisciplinary ; Muscle Proteins - chemistry ; Muscle Proteins - metabolism ; Mutation ; Mutation - genetics ; Protein Structure, Quaternary ; Proteins ; Retrovirus ; RNA - metabolism ; Science ; Science (multidisciplinary) ; Structure in molecular biology</subject><ispartof>Nature, 2007-01, Vol.445 (7126), p.447-451</ispartof><rights>Springer Nature Limited 2006</rights><rights>2007 INIST-CNRS</rights><rights>COPYRIGHT 2007 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Jan 25, 2007</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c714t-5c3c90595959d6d5e0e3a6ab459e9d6f5f37319957c5c3030771faff29f597173</citedby><cites>FETCH-LOGICAL-c714t-5c3c90595959d6d5e0e3a6ab459e9d6f5f37319957c5c3030771faff29f597173</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nature05492$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nature05492$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18453641$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17187054$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Prochnow, Courtney</creatorcontrib><creatorcontrib>Bransteitter, Ronda</creatorcontrib><creatorcontrib>Klein, Michael G.</creatorcontrib><creatorcontrib>Goodman, Myron F.</creatorcontrib><creatorcontrib>Chen, Xiaojiang S.</creatorcontrib><title>The APOBEC-2 crystal structure and functional implications for the deaminase AID</title><title>Nature</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA
1
,
2
. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies
3
, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus
4
,
5
,
6
,
7
. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long α-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.</description><subject>Amino Acid Sequence</subject><subject>APOBEC Deaminases</subject><subject>Binding Sites</subject><subject>Biological and medical sciences</subject><subject>Crystal structure</subject><subject>Crystalline structure</subject><subject>Crystallography, X-Ray</subject><subject>Cytidine Deaminase - chemistry</subject><subject>Cytidine Deaminase - genetics</subject><subject>Cytidine Deaminase - metabolism</subject><subject>Deamination</subject><subject>Deoxyribonucleic acid</subject><subject>Dimerization</subject><subject>DNA</subject><subject>DNA - metabolism</subject><subject>Enzymes</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Hepatitis</subject><subject>Hepatitis B virus</subject><subject>Human immunodeficiency virus</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Hyper-IgM Immunodeficiency Syndrome - enzymology</subject><subject>Hyper-IgM Immunodeficiency Syndrome - genetics</subject><subject>Immunology</subject><subject>letter</subject><subject>Models, Molecular</subject><subject>Molecular biophysics</subject><subject>Molecular Sequence Data</subject><subject>multidisciplinary</subject><subject>Muscle Proteins - chemistry</subject><subject>Muscle Proteins - metabolism</subject><subject>Mutation</subject><subject>Mutation - genetics</subject><subject>Protein Structure, Quaternary</subject><subject>Proteins</subject><subject>Retrovirus</subject><subject>RNA - metabolism</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Structure in molecular biology</subject><issn>0028-0836</issn><issn>1476-4687</issn><issn>1476-4687</issn><issn>1476-4679</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BEC</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqF0s-LEzEUB_AgiltXT95lEBREZ00mv4-1rlpY3EUrHkM2k9QsM5lukgH3vze1hW6lUnIIST7vG3g8AJ4jeIYgFu-DzmO0kBLZPAATRDirCRP8IZhA2IgaCsxOwJOUbiCEFHHyGJwgjgQvFRNwtfhlq-nV5YfzWd1UJt6lrLsq5TiadWqlQ1u5MZjsh1AefL_qvNHrU6rcEKtcylurex90KkHzj0_BI6e7ZJ9t91Pw49P5Yvalvrj8PJ9NL2rDEck1NdhISOV6taylFlqsmb4mVNpy4ajDHCMpKTeFQgw5R04710hHJUccn4LXm9xVHG5Hm7LqfTK263Sww5gUE5IwhNFRiFkjSYPIUdggJAVEzVFYGJGYywJf_gNvhjGWPpYwSGiDmcQF1Ru01J1VPrghR22WNtiouyFY58v1FAlKiMAE7UL3vFn5W3UfnR1AZbW29-Zg6pu9gmKy_Z2XekxJzb9_27dv_2-ni5-zrwe1iUNK0Tq1ir7X8U4hqNYDrO4NcNEvti0br3vb7ux2Ygt4tQU6Gd25qIPxaecEoZj9_fbdxqXyFJY27np_6N8_pxIBOA</recordid><startdate>20070125</startdate><enddate>20070125</enddate><creator>Prochnow, Courtney</creator><creator>Bransteitter, Ronda</creator><creator>Klein, Michael G.</creator><creator>Goodman, Myron F.</creator><creator>Chen, Xiaojiang S.</creator><general>Nature Publishing Group UK</general><general>Nature Publishing</general><general>Nature Publishing Group</general><scope>IQODW</scope><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>ATWCN</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T5</scope><scope>7TG</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88G</scope><scope>88I</scope><scope>8AF</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2M</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PSYQQ</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>R05</scope><scope>RC3</scope><scope>S0X</scope><scope>SOI</scope><scope>7SC</scope><scope>7SP</scope><scope>7SR</scope><scope>7TB</scope><scope>7U5</scope><scope>8BQ</scope><scope>F28</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>7X8</scope></search><sort><creationdate>20070125</creationdate><title>The APOBEC-2 crystal structure and functional implications for the deaminase AID</title><author>Prochnow, Courtney ; Bransteitter, Ronda ; Klein, Michael G. ; Goodman, Myron F. ; Chen, Xiaojiang S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c714t-5c3c90595959d6d5e0e3a6ab459e9d6f5f37319957c5c3030771faff29f597173</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Amino Acid Sequence</topic><topic>APOBEC Deaminases</topic><topic>Binding Sites</topic><topic>Biological and medical sciences</topic><topic>Crystal structure</topic><topic>Crystalline structure</topic><topic>Crystallography, X-Ray</topic><topic>Cytidine Deaminase - chemistry</topic><topic>Cytidine Deaminase - genetics</topic><topic>Cytidine Deaminase - metabolism</topic><topic>Deamination</topic><topic>Deoxyribonucleic acid</topic><topic>Dimerization</topic><topic>DNA</topic><topic>DNA - metabolism</topic><topic>Enzymes</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Hepatitis</topic><topic>Hepatitis B virus</topic><topic>Human immunodeficiency virus</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Hyper-IgM Immunodeficiency Syndrome - enzymology</topic><topic>Hyper-IgM Immunodeficiency Syndrome - genetics</topic><topic>Immunology</topic><topic>letter</topic><topic>Models, Molecular</topic><topic>Molecular biophysics</topic><topic>Molecular Sequence Data</topic><topic>multidisciplinary</topic><topic>Muscle Proteins - chemistry</topic><topic>Muscle Proteins - metabolism</topic><topic>Mutation</topic><topic>Mutation - genetics</topic><topic>Protein Structure, Quaternary</topic><topic>Proteins</topic><topic>Retrovirus</topic><topic>RNA - metabolism</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Structure in molecular biology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Prochnow, Courtney</creatorcontrib><creatorcontrib>Bransteitter, Ronda</creatorcontrib><creatorcontrib>Klein, Michael G.</creatorcontrib><creatorcontrib>Goodman, Myron F.</creatorcontrib><creatorcontrib>Chen, Xiaojiang S.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Middle School</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Psychology Database (Alumni)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>eLibrary</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><jtitle>Nature</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Prochnow, Courtney</au><au>Bransteitter, Ronda</au><au>Klein, Michael G.</au><au>Goodman, Myron F.</au><au>Chen, Xiaojiang S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The APOBEC-2 crystal structure and functional implications for the deaminase AID</atitle><jtitle>Nature</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2007-01-25</date><risdate>2007</risdate><volume>445</volume><issue>7126</issue><spage>447</spage><epage>451</epage><pages>447-451</pages><issn>0028-0836</issn><issn>1476-4687</issn><eissn>1476-4687</eissn><eissn>1476-4679</eissn><coden>NATUAS</coden><abstract>APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA
1
,
2
. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies
3
, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus
4
,
5
,
6
,
7
. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long α-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>17187054</pmid><doi>10.1038/nature05492</doi><tpages>5</tpages></addata></record> |
fulltext | fulltext |
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ispartof | Nature, 2007-01, Vol.445 (7126), p.447-451 |
issn | 0028-0836 1476-4687 1476-4687 1476-4679 |
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source | MEDLINE; Single Title from Nature Journals; SpringerLink Journals - AutoHoldings |
subjects | Amino Acid Sequence APOBEC Deaminases Binding Sites Biological and medical sciences Crystal structure Crystalline structure Crystallography, X-Ray Cytidine Deaminase - chemistry Cytidine Deaminase - genetics Cytidine Deaminase - metabolism Deamination Deoxyribonucleic acid Dimerization DNA DNA - metabolism Enzymes Fundamental and applied biological sciences. Psychology Hepatitis Hepatitis B virus Human immunodeficiency virus Humanities and Social Sciences Humans Hyper-IgM Immunodeficiency Syndrome - enzymology Hyper-IgM Immunodeficiency Syndrome - genetics Immunology letter Models, Molecular Molecular biophysics Molecular Sequence Data multidisciplinary Muscle Proteins - chemistry Muscle Proteins - metabolism Mutation Mutation - genetics Protein Structure, Quaternary Proteins Retrovirus RNA - metabolism Science Science (multidisciplinary) Structure in molecular biology |
title | The APOBEC-2 crystal structure and functional implications for the deaminase AID |
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