Substrate Specificity and Assembly of the Catalytic Center Derived from two Structures of Ligated Uridylate Kinase
Two crystal structures of ligated uridylate kinase fromSaccharomyces cerevisiaewere determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMp and ADP at the NMP site. Cocrystallization with ADP gave rise to a...
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| Veröffentlicht in: | Journal of molecular biology 1995-03, Vol.246 (4), p.522-530 |
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| creator | Muüller-Dieckmann, Hans-Joachim Schulz, Georg E. |
| description | Two crystal structures of ligated uridylate kinase fromSaccharomyces cerevisiaewere determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMp and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined toR-factors of 17.8% and 19.6% at resolutions of 2.1 Å and 1.9 Å, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule. |
| doi_str_mv | 10.1006/jmbi.1994.0104 |
| format | Article |
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The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMp and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined toR-factors of 17.8% and 19.6% at resolutions of 2.1 Å and 1.9 Å, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1006/jmbi.1994.0104</identifier><identifier>PMID: 7877173</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>adenosine diphosphate ; Adenosine Diphosphate - metabolism ; adenosine monophosphate ; Adenosine Monophosphate - metabolism ; Amino Acid Sequence ; Binding Sites ; Catalysis ; catalytic center ; crystal structure ; Crystallization ; enzyme activity ; induced-fit ; kinases ; Models, Molecular ; molecular conformation ; Molecular Sequence Data ; Nucleoside-Phosphate Kinase - metabolism ; pdb/1uky ; pdb/1ukz ; Protein Structure, Secondary ; refined X-ray structure ; Saccharomyces cerevisiae ; Substrate Specificity ; Uridine Monophosphate - metabolism ; uridylate kinase ; X-ray diffraction</subject><ispartof>Journal of molecular biology, 1995-03, Vol.246 (4), p.522-530</ispartof><rights>1995 Academic Press</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c309t-45fe7efd3e87be6ed1accb3b71ae6dcc45640eaf9fdf73acf2b3a3a8f8f8b6e83</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1006/jmbi.1994.0104$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/7877173$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Muüller-Dieckmann, Hans-Joachim</creatorcontrib><creatorcontrib>Schulz, Georg E.</creatorcontrib><title>Substrate Specificity and Assembly of the Catalytic Center Derived from two Structures of Ligated Uridylate Kinase</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Two crystal structures of ligated uridylate kinase fromSaccharomyces cerevisiaewere determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMp and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined toR-factors of 17.8% and 19.6% at resolutions of 2.1 Å and 1.9 Å, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule.</description><subject>adenosine diphosphate</subject><subject>Adenosine Diphosphate - metabolism</subject><subject>adenosine monophosphate</subject><subject>Adenosine Monophosphate - metabolism</subject><subject>Amino Acid Sequence</subject><subject>Binding Sites</subject><subject>Catalysis</subject><subject>catalytic center</subject><subject>crystal structure</subject><subject>Crystallization</subject><subject>enzyme activity</subject><subject>induced-fit</subject><subject>kinases</subject><subject>Models, Molecular</subject><subject>molecular conformation</subject><subject>Molecular Sequence Data</subject><subject>Nucleoside-Phosphate Kinase - metabolism</subject><subject>pdb/1uky</subject><subject>pdb/1ukz</subject><subject>Protein Structure, Secondary</subject><subject>refined X-ray structure</subject><subject>Saccharomyces cerevisiae</subject><subject>Substrate Specificity</subject><subject>Uridine Monophosphate - metabolism</subject><subject>uridylate kinase</subject><subject>X-ray diffraction</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1995</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkTtv2zAURomiReqmXbsV5dRNzqUoidQYuE_EQAbHM8HHZcpAD5ekUujfV4KNbkXBgcM991zg-wh5z2DLAJqbp96ELWvbagsMqhdkw0C2hWy4fEk2AGVZlJI3r8mblJ4AoOaVvCJXQgrBBN-QeJhMylFnpIcT2uCDDXmmenD0NiXsTTfT0dP8E-lOZ93NOVi6wyFjpJ8xhmd01Mexp_n3SA85TjZPEdO6sw-Pi9bRYwxu7tYLd2HQCd-SV153Cd9d_mty_PrlYfe92N9_-7G73ReWQ5uLqvYo0DuOUhhs0DFtreFGMI2Ns7aqmwpQ-9Y7L7i2vjRccy398kyDkl-TT2fvKY6_JkxZ9SFZ7Do94DgltSRQy1bCf0HWtC2wcjVuz6CNY0oRvTrF0Os4KwZqbUOtbai1DbW2sSx8uJgn06P7i1_iX-Yfz3OvR6UfY0jqeCiBcWD1IhBiIeSZwCWp54BRJRtwsOhCRJuVG8O_jv8By-qlaQ</recordid><startdate>19950303</startdate><enddate>19950303</enddate><creator>Muüller-Dieckmann, Hans-Joachim</creator><creator>Schulz, Georg E.</creator><general>Elsevier Ltd</general><scope>FBQ</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>M7N</scope><scope>7X8</scope></search><sort><creationdate>19950303</creationdate><title>Substrate Specificity and Assembly of the Catalytic Center Derived from two Structures of Ligated Uridylate Kinase</title><author>Muüller-Dieckmann, Hans-Joachim ; Schulz, Georg E.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c309t-45fe7efd3e87be6ed1accb3b71ae6dcc45640eaf9fdf73acf2b3a3a8f8f8b6e83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1995</creationdate><topic>adenosine diphosphate</topic><topic>Adenosine Diphosphate - metabolism</topic><topic>adenosine monophosphate</topic><topic>Adenosine Monophosphate - metabolism</topic><topic>Amino Acid Sequence</topic><topic>Binding Sites</topic><topic>Catalysis</topic><topic>catalytic center</topic><topic>crystal structure</topic><topic>Crystallization</topic><topic>enzyme activity</topic><topic>induced-fit</topic><topic>kinases</topic><topic>Models, Molecular</topic><topic>molecular conformation</topic><topic>Molecular Sequence Data</topic><topic>Nucleoside-Phosphate Kinase - metabolism</topic><topic>pdb/1uky</topic><topic>pdb/1ukz</topic><topic>Protein Structure, Secondary</topic><topic>refined X-ray structure</topic><topic>Saccharomyces cerevisiae</topic><topic>Substrate Specificity</topic><topic>Uridine Monophosphate - metabolism</topic><topic>uridylate kinase</topic><topic>X-ray diffraction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Muüller-Dieckmann, Hans-Joachim</creatorcontrib><creatorcontrib>Schulz, Georg E.</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Muüller-Dieckmann, Hans-Joachim</au><au>Schulz, Georg E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Substrate Specificity and Assembly of the Catalytic Center Derived from two Structures of Ligated Uridylate Kinase</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>1995-03-03</date><risdate>1995</risdate><volume>246</volume><issue>4</issue><spage>522</spage><epage>530</epage><pages>522-530</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Two crystal structures of ligated uridylate kinase fromSaccharomyces cerevisiaewere determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMp and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined toR-factors of 17.8% and 19.6% at resolutions of 2.1 Å and 1.9 Å, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>7877173</pmid><doi>10.1006/jmbi.1994.0104</doi><tpages>9</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0022-2836 |
| ispartof | Journal of molecular biology, 1995-03, Vol.246 (4), p.522-530 |
| issn | 0022-2836 1089-8638 |
| language | eng |
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| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | adenosine diphosphate Adenosine Diphosphate - metabolism adenosine monophosphate Adenosine Monophosphate - metabolism Amino Acid Sequence Binding Sites Catalysis catalytic center crystal structure Crystallization enzyme activity induced-fit kinases Models, Molecular molecular conformation Molecular Sequence Data Nucleoside-Phosphate Kinase - metabolism pdb/1uky pdb/1ukz Protein Structure, Secondary refined X-ray structure Saccharomyces cerevisiae Substrate Specificity Uridine Monophosphate - metabolism uridylate kinase X-ray diffraction |
| title | Substrate Specificity and Assembly of the Catalytic Center Derived from two Structures of Ligated Uridylate Kinase |
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