DNA Binding of PhoB and its Interaction with RNA Polymerase
We have identified the DNA-binding domain (DBD) of an Escherichia coliactivator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the σ 70subunit. Assuming that the PhoB DBD is st...
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| Veröffentlicht in: | Journal of molecular biology 1996-05, Vol.259 (1), p.15-26 |
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| container_title | Journal of molecular biology |
| container_volume | 259 |
| creator | Makino, Kozo Amemura, Mitsuko Kawamoto, Takeshi Kimura, Sigenobu Shinagawa, Hideo Nakata, Atsuo Suzuki, Masashi |
| description | We have identified the DNA-binding domain (DBD) of an
Escherichia coliactivator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the σ
70subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the
pstSpromoter. The
pstSpromoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed. |
| doi_str_mv | 10.1006/jmbi.1996.0298 |
| format | Article |
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Escherichia coliactivator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the σ
70subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the
pstSpromoter. The
pstSpromoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1006/jmbi.1996.0298</identifier><identifier>PMID: 8648643</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Base Sequence ; Binding Sites ; Carrier Proteins - chemistry ; Carrier Proteins - genetics ; DNA bending ; DNA recognition ; DNA, Bacterial - chemistry ; DNA, Bacterial - metabolism ; DNA-Directed RNA Polymerases - metabolism ; Electrophoresis - methods ; Escherichia coli ; Escherichia coli - chemistry ; Escherichia coli Proteins ; gene regulation ; histone H5 ; Membrane Proteins - chemistry ; Membrane Proteins - genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Periplasmic Binding Proteins ; Phosphate-Binding Proteins ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; Recombinant Proteins - chemistry ; Recombinant Proteins - genetics ; Recombinant Proteins - metabolism ; Sequence Deletion ; Sequence Homology, Amino Acid ; sigma factor</subject><ispartof>Journal of molecular biology, 1996-05, Vol.259 (1), p.15-26</ispartof><rights>1996 Academic Press</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c370t-bbc213f23fc216bb2a074df884445eb6fe7e61569d6a7f5fac46d535fb7e72453</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0022283696902983$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27903,27904,65308</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/8648643$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Makino, Kozo</creatorcontrib><creatorcontrib>Amemura, Mitsuko</creatorcontrib><creatorcontrib>Kawamoto, Takeshi</creatorcontrib><creatorcontrib>Kimura, Sigenobu</creatorcontrib><creatorcontrib>Shinagawa, Hideo</creatorcontrib><creatorcontrib>Nakata, Atsuo</creatorcontrib><creatorcontrib>Suzuki, Masashi</creatorcontrib><title>DNA Binding of PhoB and its Interaction with RNA Polymerase</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>We have identified the DNA-binding domain (DBD) of an
Escherichia coliactivator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the σ
70subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the
pstSpromoter. The
pstSpromoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed.</description><subject>Amino Acid Sequence</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Base Sequence</subject><subject>Binding Sites</subject><subject>Carrier Proteins - chemistry</subject><subject>Carrier Proteins - genetics</subject><subject>DNA bending</subject><subject>DNA recognition</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - metabolism</subject><subject>DNA-Directed RNA Polymerases - metabolism</subject><subject>Electrophoresis - methods</subject><subject>Escherichia coli</subject><subject>Escherichia coli - chemistry</subject><subject>Escherichia coli Proteins</subject><subject>gene regulation</subject><subject>histone H5</subject><subject>Membrane Proteins - chemistry</subject><subject>Membrane Proteins - genetics</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Nucleic Acid Conformation</subject><subject>Periplasmic Binding Proteins</subject><subject>Phosphate-Binding Proteins</subject><subject>Promoter Regions, Genetic</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Recombinant Proteins - chemistry</subject><subject>Recombinant Proteins - genetics</subject><subject>Recombinant Proteins - metabolism</subject><subject>Sequence Deletion</subject><subject>Sequence Homology, Amino Acid</subject><subject>sigma factor</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1996</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1Lw0AQhhdRaq1evQl78pa4m81-BE9t_SoULaLnJdnM2i1NUrOp0n_vhhZvIgwMzDzzwjwIXVISU0LEzaoqXEyzTMQkydQRGlKiskgJpo7RkJAkiRLFxCk6835FCOEsVQM0UCINxYbo9u55jCeuLl39gRuLF8tmgvO6xK7zeFZ30Oamc02Nv123xK8BXjTrXRXGHs7Ric3XHi4OfYTeH-7fpk_R_OVxNh3PI8Mk6aKiMAllNmE2dFEUSU5kWlql0jTlUAgLEgTlIitFLi23uUlFyRm3hQSZpJyN0PU-d9M2n1vwna6cN7Be5zU0W6-lIjI8-j9IuWSKExHAeA-atvG-Bas3ravydqcp0b1W3WvVvVbdaw0HV4fkbVFB-YsfPIa92u8hePhy0GpvHNQGSteC6XTZuL-ifwD6i4TB</recordid><startdate>19960531</startdate><enddate>19960531</enddate><creator>Makino, Kozo</creator><creator>Amemura, Mitsuko</creator><creator>Kawamoto, Takeshi</creator><creator>Kimura, Sigenobu</creator><creator>Shinagawa, Hideo</creator><creator>Nakata, Atsuo</creator><creator>Suzuki, Masashi</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>7QL</scope><scope>7TM</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>19960531</creationdate><title>DNA Binding of PhoB and its Interaction with RNA Polymerase</title><author>Makino, Kozo ; Amemura, Mitsuko ; Kawamoto, Takeshi ; Kimura, Sigenobu ; Shinagawa, Hideo ; Nakata, Atsuo ; Suzuki, Masashi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c370t-bbc213f23fc216bb2a074df884445eb6fe7e61569d6a7f5fac46d535fb7e72453</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1996</creationdate><topic>Amino Acid Sequence</topic><topic>Bacterial Proteins - chemistry</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Base Sequence</topic><topic>Binding Sites</topic><topic>Carrier Proteins - chemistry</topic><topic>Carrier Proteins - genetics</topic><topic>DNA bending</topic><topic>DNA recognition</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - metabolism</topic><topic>DNA-Directed RNA Polymerases - metabolism</topic><topic>Electrophoresis - methods</topic><topic>Escherichia coli</topic><topic>Escherichia coli - chemistry</topic><topic>Escherichia coli Proteins</topic><topic>gene regulation</topic><topic>histone H5</topic><topic>Membrane Proteins - chemistry</topic><topic>Membrane Proteins - genetics</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Mutation</topic><topic>Nucleic Acid Conformation</topic><topic>Periplasmic Binding Proteins</topic><topic>Phosphate-Binding Proteins</topic><topic>Promoter Regions, Genetic</topic><topic>Protein Binding</topic><topic>Protein Conformation</topic><topic>Recombinant Proteins - chemistry</topic><topic>Recombinant Proteins - genetics</topic><topic>Recombinant Proteins - metabolism</topic><topic>Sequence Deletion</topic><topic>Sequence Homology, Amino Acid</topic><topic>sigma factor</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Makino, Kozo</creatorcontrib><creatorcontrib>Amemura, Mitsuko</creatorcontrib><creatorcontrib>Kawamoto, Takeshi</creatorcontrib><creatorcontrib>Kimura, Sigenobu</creatorcontrib><creatorcontrib>Shinagawa, Hideo</creatorcontrib><creatorcontrib>Nakata, Atsuo</creatorcontrib><creatorcontrib>Suzuki, Masashi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Nucleic Acids Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Makino, Kozo</au><au>Amemura, Mitsuko</au><au>Kawamoto, Takeshi</au><au>Kimura, Sigenobu</au><au>Shinagawa, Hideo</au><au>Nakata, Atsuo</au><au>Suzuki, Masashi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA Binding of PhoB and its Interaction with RNA Polymerase</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>1996-05-31</date><risdate>1996</risdate><volume>259</volume><issue>1</issue><spage>15</spage><epage>26</epage><pages>15-26</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>We have identified the DNA-binding domain (DBD) of an
Escherichia coliactivator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the σ
70subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the
pstSpromoter. The
pstSpromoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>8648643</pmid><doi>10.1006/jmbi.1996.0298</doi><tpages>12</tpages></addata></record> |
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| ispartof | Journal of molecular biology, 1996-05, Vol.259 (1), p.15-26 |
| issn | 0022-2836 1089-8638 |
| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Amino Acid Sequence Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Base Sequence Binding Sites Carrier Proteins - chemistry Carrier Proteins - genetics DNA bending DNA recognition DNA, Bacterial - chemistry DNA, Bacterial - metabolism DNA-Directed RNA Polymerases - metabolism Electrophoresis - methods Escherichia coli Escherichia coli - chemistry Escherichia coli Proteins gene regulation histone H5 Membrane Proteins - chemistry Membrane Proteins - genetics Models, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation Periplasmic Binding Proteins Phosphate-Binding Proteins Promoter Regions, Genetic Protein Binding Protein Conformation Recombinant Proteins - chemistry Recombinant Proteins - genetics Recombinant Proteins - metabolism Sequence Deletion Sequence Homology, Amino Acid sigma factor |
| title | DNA Binding of PhoB and its Interaction with RNA Polymerase |
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