{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T08:47:18Z","timestamp":1791103638707,"version":"4.1.0"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2013,11,22]],"date-time":"2013-11-22T00:00:00Z","timestamp":1385078400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0081324","type":"journal-article","created":{"date-parts":[[2013,11,22]],"date-time":"2013-11-22T22:57:05Z","timestamp":1385161025000},"page":"e81324","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":47,"title":["Investigating the Allosteric Regulation of YfiN from Pseudomonas aeruginosa: Clues from the Structure of the Catalytic Domain"],"prefix":"10.1371","volume":"8","author":[{"given":"Giorgio","family":"Giardina","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Paiardini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Fernicola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Franceschini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serena","family":"Rinaldo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Stelitano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Cutruzzol\u00e0","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2013,11,22]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1038\/nrmicro2203","article-title":"Structural and mechanistic determinants of c-di-GMP signalling","volume":"7","author":"T Schirmer","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.mib.2011.12.008","article-title":"You\u2019ve come a long way: c-di-GMP signaling","volume":"15","author":"H Sondermann","year":"2012","journal-title":"Curr Opin Microbiol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1128\/AAC.02499-12","article-title":"Bis-(3\u2019-5&apos;)-Cyclic Dimeric GMP Regulates Antimicrobial Peptide Resistance in Pseudomonas aeruginosa","volume":"57","author":"SL Chua","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/MMBR.00043-12","article-title":"Cyclic di-GMP: the first 25 years of a universal bacterial second messenger","volume":"77","author":"U R\u00f6mling","year":"2013","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1128\/MMBR.60.3.539-574.1996","article-title":"Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia","volume":"60","author":"JR Govan","year":"1996","journal-title":"Microbiol Rev"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1086\/598644","article-title":"Small-colony variants of Pseudomonas aeruginosa in cystic fibrosis","volume":"29","author":"S H\u00e4ussler","year":"1999","journal-title":"Clin Infect Dis"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1099\/jmm.0.05069-0","article-title":"Highly adherent small-colony variants of Pseudomonas aeruginosa in cystic fibrosis lung infection","volume":"52","author":"S H\u00e4ussler","year":"2003","journal-title":"J Med Microbiol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1111\/j.1462-2920.2004.00618.x","article-title":"Biofilm formation by the small colony variant phenotype of Pseudomonas aeruginosa","volume":"6","author":"S H\u00e4ussler","year":"2004","journal-title":"Environ Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"8487","DOI":"10.1073\/pnas.0602138103","article-title":"Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients","volume":"103","author":"EE Smith","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"3492","DOI":"10.1128\/JB.00119-09","article-title":"Pseudomonas aeruginosa rugose small-colony variants have adaptations that likely promote persistence in the cystic fibrosis lung","volume":"191","author":"M Starkey","year":"2009","journal-title":"J Bacteriol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1111\/j.1462-2920.2007.01366.x","article-title":"Pseudomonas aeruginosa cupA-encoded fimbriae expression is regulated by a GGDEF and EAL domain-dependent modulation of the intracellular level of cyclic diguanylate","volume":"9","author":"A Meissner","year":"2007","journal-title":"Environ Microbiol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1086\/598644","article-title":"Small-Colony Variants of Pseudomonas aeruginosa in Cystic Fibrosis","volume":"29","author":"M Rohde","year":"1999","journal-title":"Clin Infect Dis"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/416740a","article-title":"Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation","volume":"416","author":"E Drenkard","year":"2002","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e1000804","DOI":"10.1371\/journal.ppat.1000804","article-title":"YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa","volume":"6","author":"JG Malone","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1128\/AAC.01278-06","article-title":"Development and persistence of antimicrobial resistance in Pseudomonas aeruginosa: a longitudinal observation in mechanically ventilated patients","volume":"51","author":"A Reinhardt","year":"2007","journal-title":"Antimicrob Agents Chemother"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"6191","DOI":"10.1128\/JB.01651-09","article-title":"Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis","volume":"192","author":"LR Mulcahy","year":"2010","journal-title":"J Bacteriol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1073\/pnas.0511090103","article-title":"Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3\u2019-5&apos;)-cyclic-GMP in virulence","volume":"103","author":"H Kulasakara","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1111\/j.1758-2229.2010.00171.x","article-title":"Tyrosine Phosphatase TpbA of Pseudomonas aeruginosa Controls Extracellular DNA via Cyclic Diguanylic Acid Concentrations","volume":"2","author":"A Ueda","year":"2010","journal-title":"Environ Microbiol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1534\/genetics.109.107110","article-title":"Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation","volume":"183","author":"MJ McDonald","year":"2009","journal-title":"Genetics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e1002760","DOI":"10.1371\/journal.ppat.1002760","article-title":"The YfiBNR Signal Transduction Mechanism Reveals Novel Targets for the Evolution of Persistent Pseudomonas aeruginosa in Cystic Fibrosis Airways","volume":"8","author":"JG Malone","year":"2012","journal-title":"PLoS Pathog"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"20632","DOI":"10.1073\/pnas.1217993109","article-title":"Self-produced exopolysaccharide is a signal that stimulates biofilm formation in Pseudomonas aeruginosa","volume":"109","author":"Y Irie","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1042\/BST0390294","article-title":"The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms","volume":"39","author":"G Giardina","year":"2011","journal-title":"Biochem Soc Trans"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e79","DOI":"10.1093\/nar\/gkt028","article-title":"Probing the activity of diguanylate cyclases and c-di-GMP phosphodiesterases in real-time by CD spectroscopy","volume":"41","author":"V Stelitano","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e1000588","DOI":"10.1371\/journal.pbio.1000588","article-title":"Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis","volume":"9","author":"MV Navarro","year":"2011","journal-title":"PLoS Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nprot.2009.2","article-title":"Protein structure prediction on the Web: a case study using the Phyre server","volume":"4","author":"MJE Sternberg","year":"2009","journal-title":"Nat Protoc"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/prot.22499","article-title":"Fast and accurate automatic structure prediction with HHpred","volume":"77","author":"A Hildebrand","year":"2009","journal-title":"Proteins"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"17084","DOI":"10.1073\/pnas.0406134101","article-title":"Structural basis of activity and allosteric control of diguanylate cyclase","volume":"101","author":"C Chan","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/j.str.2007.06.016","article-title":"Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition","volume":"15","author":"P Wassmann","year":"2007","journal-title":"Structure"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/j.jmb.2009.08.030","article-title":"Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR","volume":"393","author":"N De","year":"2009","journal-title":"J Mol Biol"},{"key":"ref30","first-page":"601","article-title":"Phosphorylation-Independent Regulation of the Diguanylate Cyclase WspR","volume":"6","author":"N De","year":"2008","journal-title":"PLoS Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1107\/S090744491104039X","article-title":"The structure and inhibition of a GGDEF diguanylate cyclase complexed with (c-di-GMP) 2 at the active site","volume":"67","author":"C-Y Yang","year":"2011","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1007\/s10969-012-9136-4","article-title":"Crystal structure of a catalytically active GG(D\/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product","volume":"13","author":"SM Vorobiev","year":"2012","journal-title":"J Struct Funct Genomics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"23582","DOI":"10.1074\/jbc.M112.375378","article-title":"Structure of the cytoplasmic region of PelD, a degenerate diguanylate cyclase receptor that regulates exopolysaccharide production in Pseudomonas aeruginosa","volume":"287","author":"JC Whitney","year":"2012","journal-title":"J Biol Chem"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.jmb.2010.03.007","article-title":"Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins","volume":"398","author":"J Ko","year":"2010","journal-title":"J Mol Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/S0022-2836(02)00263-2","article-title":"Cation\u2013\u03c0\/H-bond Stair Motifs at Protein\u2013DNA","volume":"319","author":"M Rooman","year":"2002","journal-title":"Interfaces - J Mol Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"4109","DOI":"10.1093\/nar\/gkh733","article-title":"Interaction of DNA with clusters of amino acids in proteins","volume":"32","author":"R Sathyapriya","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/j.cell.2006.06.058","article-title":"The HAMP domain structure implies helix rotation in transmembrane signaling","volume":"126","author":"M Hulko","year":"2006","journal-title":"Cell"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3461","DOI":"10.1073\/pnas.0808933106","article-title":"LapD is a bis-(3\u2019,5&apos;)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0 \u2013 1","volume":"106","author":"PD Newell","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e1001479","DOI":"10.1371\/journal.pbio.1001479","article-title":"HAMP Domain Conformers That Propagate Opposite Signals in Bacterial Chemoreceptors","volume":"11","author":"MV Airola","year":"2013","journal-title":"PLoS Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"39189","DOI":"10.1074\/jbc.M305864200","article-title":"The structure of the periplasmic ligand-binding domain of the sensor kinase CitA reveals the first extracellular PAS domain","volume":"278","author":"S Reinelt","year":"2003","journal-title":"J Biol Chem"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"10902","DOI":"10.1073\/pnas.1001656107","article-title":"Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis","volume":"107","author":"I Maslennikov","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"3090","DOI":"10.1103\/PhysRevLett.79.3090","article-title":"Gaussian Dynamics of Folded","volume":"79","author":"T Haliloglu","year":"1997","journal-title":"Proteins - Phys Rev Lett"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/S0006-3495(01)76033-X","article-title":"Anisotropy of fluctuation dynamics of proteins with an elastic network model","volume":"80","author":"AR Atilgan","year":"2001","journal-title":"Biophys J"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1016\/S0006-3495(00)76713-0","article-title":"Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling","volume":"78","author":"P Schuck","year":"2000","journal-title":"Biophys J"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1107\/S0021889893005588","article-title":"Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants","volume":"26","author":"W Kabsch","year":"1993","journal-title":"J Appl Crystallogr"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1107\/S0907444909042589","article-title":"Molecular replacement with MOLREP","volume":"66","author":"A Vagin","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: model-building tools for molecular graphics","volume":"60","author":"P Emsley","year":"2004","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1107\/S0907444996012255","article-title":"Refinement of macromolecular structures by the maximum-likelihood method","volume":"53","author":"GN Murshudov","year":"1997","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"RA Laskowski","year":"1993","journal-title":"J Appl Crystallography"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"W375","DOI":"10.1093\/nar\/gkm216","article-title":"MolProbity: all-atom contacts and structure validation for proteins and nucleic acids","volume":"35","author":"IW Davis","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"8971","DOI":"10.1021\/bi300792h","article-title":"Interactions outside the boundaries of the canonical binding groove of a PDZ domain influence ligand binding","volume":"51","author":"CN Chi","year":"2012","journal-title":"Biochemistry"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"JD Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"ref54","first-page":"473","article-title":"DSC: public domain protein secondary structure predication","volume":"13","author":"RD King","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"ref55","first-page":"53","article-title":"PHD--an automatic mail server for protein secondary structure prediction","volume":"10","author":"B Rost","year":"1994","journal-title":"Comput Appl Biosci"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"DT Jones","year":"1999","journal-title":"J Mol Biol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1002\/prot.340230306","article-title":"Evaluation of comparative protein modeling by MODELLER","volume":"23","author":"A Sali","year":"1995","journal-title":"Proteins"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1093\/bioinformatics\/btk023","article-title":"OPM: orientations of proteins in membranes database","volume":"22","author":"MA Lomize","year":"2006","journal-title":"Bioinformatics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1002\/prot.340170404","article-title":"Recognition of errors in three-dimensional structures of proteins","volume":"17","author":"MJ Sippl","year":"1993","journal-title":"Proteins"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1002\/prot.21613","article-title":"HingeProt: automated prediction of hinges in protein structures","volume":"70","author":"U Emekli","year":"2008","journal-title":"Proteins"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"W50","DOI":"10.1093\/nar\/gki416","article-title":"CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology","volume":"33","author":"A Paiardini","year":"2005","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0081324","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T13:30:52Z","timestamp":1597066252000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0081324"}},"subtitle":[],"editor":[{"given":"Renwick","family":"Dobson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,11,22]]},"references-count":61,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2013,11,22]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0081324","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,22]]}}}