Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus

The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8 Å and 2.5 Å, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolo...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Journal of molecular biology 2003-07, Vol.330 (5), p.1087-1099
Hauptverfasser: Criswell, Angela R., Bae, Euiyoung, Stec, Boguslaw, Konisky, Jordan, Phillips Jr, George N.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 1099
container_issue 5
container_start_page 1087
container_title Journal of molecular biology
container_volume 330
creator Criswell, Angela R.
Bae, Euiyoung
Stec, Boguslaw
Konisky, Jordan
Phillips Jr, George N.
description The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8 Å and 2.5 Å, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central β-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M. voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the “invariant” Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S. acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S. acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.
doi_str_mv 10.1016/S0022-2836(03)00655-7
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_73477222</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0022283603006557</els_id><sourcerecordid>18858601</sourcerecordid><originalsourceid>FETCH-LOGICAL-c458t-5ea931aeb4aa57c6d13d91a0a2b6e4abb9752558f9bce17d0c0b10c9bea3b3663</originalsourceid><addsrcrecordid>eNqFkFFL5DAUhYOs6OzoT3Dp06IP1ZukSdMnGUTdRcUHFXwLSXrLZGmbMWkF_711ZlYffbpc-M458BFyROGUApVnDwCM5UxxeQz8BEAKkZc7ZEZBVbmSXP0gs09kn_xM6R8ACF6oPbJPmZJAOczI88MQRzeMEVMWmuxxibELq6VvvctMX2d3mP6_ixr7t9YMmN343qQp0MTQZcMSs2vsxzSxw9L0wQXnxnRAdhvTJjzc3jl5urp8vPiT395f_71Y3OauEGrIBZqKU4O2MEaUTtaU1xU1YJiVWBhrq1IwIVRTWYe0rMGBpeAqi4ZbLiWfk9-b3lUMLyOmQXc-OWxb02MYky55UZaMsW9BqpRYW5kTsQFdDClFbPQq-s7EN01Bf7jXa_f6Q6wGrtfup505-bUdGG2H9VdqK3sCzjcATj5ePUadnMfeYe0jukHXwX8z8Q7wh5SS</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>18858601</pqid></control><display><type>article</type><title>Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus</title><source>MEDLINE</source><source>Access via ScienceDirect (Elsevier)</source><creator>Criswell, Angela R. ; Bae, Euiyoung ; Stec, Boguslaw ; Konisky, Jordan ; Phillips Jr, George N.</creator><creatorcontrib>Criswell, Angela R. ; Bae, Euiyoung ; Stec, Boguslaw ; Konisky, Jordan ; Phillips Jr, George N.</creatorcontrib><description>The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8 Å and 2.5 Å, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central β-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M. voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the “invariant” Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S. acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S. acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/S0022-2836(03)00655-7</identifier><identifier>PMID: 12860130</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Adenosine Monophosphate - chemistry ; adenylate kinase ; Adenylate Kinase - chemistry ; Amino Acid Sequence ; Arginine - chemistry ; Binding Sites ; Crystallography, X-Ray ; DNA Mutational Analysis ; Escherichia coli - metabolism ; Hydrogen Bonding ; Ligands ; Lysine - chemistry ; Methanococcus ; Methanococcus - enzymology ; Methanococcus thermolithotrophicus ; Methanococcus voltae ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; phosphate-binding loop ; Plasmids - metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; protein thermostability ; Sequence Homology, Amino Acid ; Temperature ; X-ray crystallography</subject><ispartof>Journal of molecular biology, 2003-07, Vol.330 (5), p.1087-1099</ispartof><rights>2003 Elsevier Science Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c458t-5ea931aeb4aa57c6d13d91a0a2b6e4abb9752558f9bce17d0c0b10c9bea3b3663</citedby><cites>FETCH-LOGICAL-c458t-5ea931aeb4aa57c6d13d91a0a2b6e4abb9752558f9bce17d0c0b10c9bea3b3663</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/S0022-2836(03)00655-7$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12860130$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Criswell, Angela R.</creatorcontrib><creatorcontrib>Bae, Euiyoung</creatorcontrib><creatorcontrib>Stec, Boguslaw</creatorcontrib><creatorcontrib>Konisky, Jordan</creatorcontrib><creatorcontrib>Phillips Jr, George N.</creatorcontrib><title>Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8 Å and 2.5 Å, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central β-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M. voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the “invariant” Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S. acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S. acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.</description><subject>Adenosine Monophosphate - chemistry</subject><subject>adenylate kinase</subject><subject>Adenylate Kinase - chemistry</subject><subject>Amino Acid Sequence</subject><subject>Arginine - chemistry</subject><subject>Binding Sites</subject><subject>Crystallography, X-Ray</subject><subject>DNA Mutational Analysis</subject><subject>Escherichia coli - metabolism</subject><subject>Hydrogen Bonding</subject><subject>Ligands</subject><subject>Lysine - chemistry</subject><subject>Methanococcus</subject><subject>Methanococcus - enzymology</subject><subject>Methanococcus thermolithotrophicus</subject><subject>Methanococcus voltae</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>phosphate-binding loop</subject><subject>Plasmids - metabolism</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Protein Structure, Tertiary</subject><subject>protein thermostability</subject><subject>Sequence Homology, Amino Acid</subject><subject>Temperature</subject><subject>X-ray crystallography</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkFFL5DAUhYOs6OzoT3Dp06IP1ZukSdMnGUTdRcUHFXwLSXrLZGmbMWkF_711ZlYffbpc-M458BFyROGUApVnDwCM5UxxeQz8BEAKkZc7ZEZBVbmSXP0gs09kn_xM6R8ACF6oPbJPmZJAOczI88MQRzeMEVMWmuxxibELq6VvvctMX2d3mP6_ixr7t9YMmN343qQp0MTQZcMSs2vsxzSxw9L0wQXnxnRAdhvTJjzc3jl5urp8vPiT395f_71Y3OauEGrIBZqKU4O2MEaUTtaU1xU1YJiVWBhrq1IwIVRTWYe0rMGBpeAqi4ZbLiWfk9-b3lUMLyOmQXc-OWxb02MYky55UZaMsW9BqpRYW5kTsQFdDClFbPQq-s7EN01Bf7jXa_f6Q6wGrtfup505-bUdGG2H9VdqK3sCzjcATj5ePUadnMfeYe0jukHXwX8z8Q7wh5SS</recordid><startdate>20030725</startdate><enddate>20030725</enddate><creator>Criswell, Angela R.</creator><creator>Bae, Euiyoung</creator><creator>Stec, Boguslaw</creator><creator>Konisky, Jordan</creator><creator>Phillips Jr, George N.</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>C1K</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>7X8</scope></search><sort><creationdate>20030725</creationdate><title>Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus</title><author>Criswell, Angela R. ; Bae, Euiyoung ; Stec, Boguslaw ; Konisky, Jordan ; Phillips Jr, George N.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c458t-5ea931aeb4aa57c6d13d91a0a2b6e4abb9752558f9bce17d0c0b10c9bea3b3663</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Adenosine Monophosphate - chemistry</topic><topic>adenylate kinase</topic><topic>Adenylate Kinase - chemistry</topic><topic>Amino Acid Sequence</topic><topic>Arginine - chemistry</topic><topic>Binding Sites</topic><topic>Crystallography, X-Ray</topic><topic>DNA Mutational Analysis</topic><topic>Escherichia coli - metabolism</topic><topic>Hydrogen Bonding</topic><topic>Ligands</topic><topic>Lysine - chemistry</topic><topic>Methanococcus</topic><topic>Methanococcus - enzymology</topic><topic>Methanococcus thermolithotrophicus</topic><topic>Methanococcus voltae</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>phosphate-binding loop</topic><topic>Plasmids - metabolism</topic><topic>Protein Binding</topic><topic>Protein Conformation</topic><topic>Protein Structure, Tertiary</topic><topic>protein thermostability</topic><topic>Sequence Homology, Amino Acid</topic><topic>Temperature</topic><topic>X-ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Criswell, Angela R.</creatorcontrib><creatorcontrib>Bae, Euiyoung</creatorcontrib><creatorcontrib>Stec, Boguslaw</creatorcontrib><creatorcontrib>Konisky, Jordan</creatorcontrib><creatorcontrib>Phillips Jr, George N.</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>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science &amp; Fisheries Abstracts (ASFA) 1: Biological Sciences &amp; Living Resources</collection><collection>Aquatic Science &amp; Fisheries Abstracts (ASFA) Professional</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Criswell, Angela R.</au><au>Bae, Euiyoung</au><au>Stec, Boguslaw</au><au>Konisky, Jordan</au><au>Phillips Jr, George N.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2003-07-25</date><risdate>2003</risdate><volume>330</volume><issue>5</issue><spage>1087</spage><epage>1099</epage><pages>1087-1099</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8 Å and 2.5 Å, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central β-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M. voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the “invariant” Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S. acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S. acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>12860130</pmid><doi>10.1016/S0022-2836(03)00655-7</doi><tpages>13</tpages></addata></record>
fulltext fulltext
identifier ISSN: 0022-2836
ispartof Journal of molecular biology, 2003-07, Vol.330 (5), p.1087-1099
issn 0022-2836
1089-8638
language eng
recordid cdi_proquest_miscellaneous_73477222
source MEDLINE; Access via ScienceDirect (Elsevier)
subjects Adenosine Monophosphate - chemistry
adenylate kinase
Adenylate Kinase - chemistry
Amino Acid Sequence
Arginine - chemistry
Binding Sites
Crystallography, X-Ray
DNA Mutational Analysis
Escherichia coli - metabolism
Hydrogen Bonding
Ligands
Lysine - chemistry
Methanococcus
Methanococcus - enzymology
Methanococcus thermolithotrophicus
Methanococcus voltae
Models, Chemical
Models, Molecular
Molecular Sequence Data
phosphate-binding loop
Plasmids - metabolism
Protein Binding
Protein Conformation
Protein Structure, Tertiary
protein thermostability
Sequence Homology, Amino Acid
Temperature
X-ray crystallography
title Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T18%3A14%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Structures%20of%20Thermophilic%20and%20Mesophilic%20Adenylate%20Kinases%20from%20the%20Genus%20Methanococcus&rft.jtitle=Journal%20of%20molecular%20biology&rft.au=Criswell,%20Angela%20R.&rft.date=2003-07-25&rft.volume=330&rft.issue=5&rft.spage=1087&rft.epage=1099&rft.pages=1087-1099&rft.issn=0022-2836&rft.eissn=1089-8638&rft_id=info:doi/10.1016/S0022-2836(03)00655-7&rft_dat=%3Cproquest_cross%3E18858601%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=18858601&rft_id=info:pmid/12860130&rft_els_id=S0022283603006557&rfr_iscdi=true