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Volumn 194, Issue 18, 2012, Pages 4837-4846

Structural insights into the regulatory mechanism of the response regulator RocR from Pseudomonas aeruginosa in cyclic Di-GMP signaling

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC DI GMP; CYCLIC GMP; PROTEIN ROCR; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

EID: 84866351420     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00560-12     Document Type: Article
Times cited : (47)

References (50)
  • 1
    • 77957820323 scopus 로고    scopus 로고
    • Regulation of response regulator autophosphorylation through interdo- main contacts
    • Barbieri CM, Mack TR, Robinson VL, Miller MT, Stock AM. 2010. Regulation of response regulator autophosphorylation through interdo- main contacts. J. Biol. Chem. 285:32325-32335.
    • (2010) J. Biol. Chem. , vol.285 , pp. 32325-32335
    • Barbieri, C.M.1    Mack, T.R.2    Robinson, V.L.3    Miller, M.T.4    Stock, A.M.5
  • 2
    • 67649295467 scopus 로고    scopus 로고
    • Structure and mechanism of a bacterial light- regulated cyclic nucleotide phosphodiesterase
    • Barends TRM, et al. 2009. Structure and mechanism of a bacterial light- regulated cyclic nucleotide phosphodiesterase. Nature 459:1015-1018.
    • (2009) Nature , vol.459 , pp. 1015-1018
    • Barends, T.R.M.1
  • 3
    • 77949880884 scopus 로고    scopus 로고
    • Receiver domain structure and function in response regulator proteins
    • Bourret RB. 2010. Receiver domain structure and function in response regulator proteins. Curr. Opin. Microbiol. 13:142-149.
    • (2010) Curr. Opin. Microbiol. , vol.13 , pp. 142-149
    • Bourret, R.B.1
  • 4
    • 0035957226 scopus 로고    scopus 로고
    • Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor
    • Chang AL, et al. 2001. Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40:3420-3426.
    • (2001) Biochemistry , vol.40 , pp. 3420-3426
    • Chang, A.L.1
  • 5
    • 0034737324 scopus 로고    scopus 로고
    • NMR structure of activated CheY
    • Cho HS, et al. 2000. NMR structure of activated CheY. J. Mol. Biol. 297:543-551.
    • (2000) J. Mol. Biol. , vol.297 , pp. 543-551
    • Cho, H.S.1
  • 6
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallogra- phy
    • Collaborative.
    • Collaborative. 1994. The CCP4 suite: programs for protein crystallogra- phy. Acta Crystallogr. Sect. D 50:760-763.
    • (1994) Acta Crystallogr. Sect. , vol.D50 , pp. 760-763
  • 7
    • 33846847846 scopus 로고    scopus 로고
    • c-di-GMP-mediated regulation of virulence and biofilm formation
    • Cotter PA, Stibitz S. 2007. c-di-GMP-mediated regulation of virulence and biofilm formation. Curr. Opin. Microbiol. 10:17-23.
    • (2007) Curr. Opin. Microbiol. , vol.10 , pp. 17-23
    • Cotter, P.A.1    Stibitz, S.2
  • 8
    • 33748337934 scopus 로고    scopus 로고
    • The Buccaneer software for automated model building. 1. Tracing protein chains
    • Cowtan K. 2006. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. Sect. D Biol. Crystallogr. 62: 1002-1011.
    • (2006) Acta Crystallogr. Sect. D Biol. Crystallogr , vol.62 , pp. 1002-1011
    • Cowtan, K.1
  • 9
    • 41749103519 scopus 로고    scopus 로고
    • Phosphorylation-independent regulation of the diguanylate cyclase WspR
    • doi:10.1371/journal.pbio.0060067
    • De N. 2008. Phosphorylation-independent regulation of the diguanylate cyclase WspR. PLoS Biol. 6:e67. doi:10.1371/journal.pbio.0060067.
    • (2008) PLoS Biol. , vol.6
    • De, N.1
  • 10
    • 0032539671 scopus 로고    scopus 로고
    • Struc-tural basis for methylesterase CheB regulation by a phosphorylation- activated domain
    • Djordjevic S, Goudreau PN, Xu Q, Stock AM, West AH. 1998. Struc- tural basis for methylesterase CheB regulation by a phosphorylation-activated domain. Proc. Natl. Acad. Sci. 95:1381-1386.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 1381-1386
    • Djordjevic, S.1    Goudreau, P.N.2    Xu, Q.3    Stock, A.M.4    West, A.H.5
  • 12
    • 33644873452 scopus 로고    scopus 로고
    • The Database of Macromolecular Motions: new features added at the decade mark
    • Flores S, et al. The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res. 34:D296-D301.
    • Nucleic Acids Res , vol.34
    • Flores, S.1
  • 13
    • 62649139615 scopus 로고    scopus 로고
    • DAMMIF, a program for rapid ab initio shape determination in small-angle scattering
    • Franke D, Svergun DI. 2009. DAMMIF, a program for rapid ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 42:342-346.
    • (2009) J. Appl. Crystallogr. , vol.42 , pp. 342-346
    • Franke, D.1    Svergun, D.I.2
  • 14
    • 0035845587 scopus 로고    scopus 로고
    • Novel domains of the prokaryotic two-component signal transduction systems
    • Galperin MY, Nikolskaya AN, Koonin EV. 2001. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol. Lett. 203:11-21.
    • (2001) FEMS Microbiol. Lett. , vol.203 , pp. 11-21
    • Galperin, M.Y.1    Nikolskaya, A.N.2    Koonin, E.V.3
  • 15
    • 71149087504 scopus 로고    scopus 로고
    • Transient non-native hydrogen bonds promote activation of a signaling protein
    • Cell
    • Gardino AK, et al. 2009. Transient non-native hydrogen bonds promote activation of a signaling protein. Cell 139:1109-1118.
    • (2009) , vol.139 , pp. 1109-1118
    • Gardino, A.K.1
  • 16
    • 0032961270 scopus 로고    scopus 로고
    • ESPript: analysis of multiple sequence alignments in PostScript
    • Gouet P, Courcelle E, Stuart DI, Métoz FM. 1999. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15:305-308.
    • (1999) Bioinformatics , vol.15 , pp. 305-308
    • Gouet, P.1    Courcelle, E.2    Stuart, D.I.3    Métoz, F.M.4
  • 17
    • 63049137897 scopus 로고    scopus 로고
    • Principles of c-di-GMP signaling in bacteria
    • Hengge R. 2009. Principles of c-di-GMP signaling in bacteria. Nat. Rev. Microbiol. 7:263-273.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 263-273
    • Hengge, R.1
  • 18
    • 76449106188 scopus 로고    scopus 로고
    • Integration, scaling, space-group assignment and post- refinement
    • Kabsch W. 2010. Integration, scaling, space-group assignment and post- refinement. Acta Crystallogr. Sect. D 66:133-144.
    • (2010) Acta Crystallogr. Sect. , vol.D66 , pp. 133-144
    • Kabsch, W.1
  • 20
    • 70350331582 scopus 로고    scopus 로고
    • Expression, purification and preliminary crystal- lographic analysis of Pseudomonas aeruginosa RocR protein
    • Kotaka M, et al. 2009. Expression, purification and preliminary crystal- lographic analysis of Pseudomonas aeruginosa RocR protein. Acta Crystal- logr. Sect. F 65:1035-1038.
    • (2009) Acta Crystal-logr. Sect. , vol.F 65 , pp. 1035-1038
    • Kotaka, M.1
  • 21
    • 0035124442 scopus 로고    scopus 로고
    • Automated matching of high- and low- resolution structural models
    • Kozin MB, Svergun DI. 2001. Automated matching of high- and low- resolution structural models. J. Appl. Crystallogr. 34:33-41.
    • (2001) J. Appl. Crystallogr. , vol.34 , pp. 33-41
    • Kozin, M.B.1    Svergun, D.I.2
  • 22
    • 34548232365 scopus 로고    scopus 로고
    • Inference of macromolecular assemblies from crystalline state
    • Krissinel E, Henrick K. 2007. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372:774-797.
    • (2007) J. Mol. Biol. , vol.372 , pp. 774-797
    • Krissinel, E.1    Henrick, K.2
  • 23
    • 14544291492 scopus 로고    scopus 로고
    • A three-component regu- latory system regulates biofilm maturation and type III secretion in Pseu- domonas aeruginosa
    • Kuchma SL, Connolly JP, O'Toole GA. 2005. A three-component regu- latory system regulates biofilm maturation and type III secretion in Pseu- domonas aeruginosa. J. Bacteriol. 187:1441-1454.
    • (2005) J. Bacteriol. , vol.187 , pp. 1441-1454
    • Kuchma, S.L.1    Connolly, J.P.2    O'toole, G.A.3
  • 24
    • 13144257722 scopus 로고    scopus 로고
    • A novel two-component system controls the expression of Pseudomonas aeruginosa fimbrial cup genes
    • Kulasekara HD, et al. 2005. A novel two-component system controls the expression of Pseudomonas aeruginosa fimbrial cup genes. Mol. Microbiol. 55:368-380.
    • (2005) Mol. Microbiol. , vol.55 , pp. 368-380
    • Kulasekara, H.D.1
  • 25
    • 0035174242 scopus 로고    scopus 로고
    • Crystal structure of an activated response regulator bound to its target
    • Lee SY, et al. 2001. Crystal structure of an activated response regulator bound to its target. Nat. Struct. Biol. 8:52-56.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 52-56
    • Lee, S.Y.1
  • 26
    • 67649746308 scopus 로고    scopus 로고
    • Crystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodi- ester bond cleavage by EAL domains
    • Minasov G, et al. 2009. Crystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodi- ester bond cleavage by EAL domains. J. Biol. Chem. 284:13174-13184.
    • (2009) J. Biol. Chem. , vol.284 , pp. 13174-13184
    • Minasov, G.1
  • 27
    • 68149172669 scopus 로고    scopus 로고
    • Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX
    • Navarro MVAS, Bae DNN, Wang Q, Sondermann H. 2009. Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX. Structure 17:1104-1116.
    • (2009) Structure , vol.17 , pp. 1104-1116
    • Navarro, M.V.A.S.1    Bae, D.N.N.2    Wang, Q.3    Sondermann, H.4
  • 28
    • 79952260048 scopus 로고    scopus 로고
    • Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis
    • doi:10.1371/journal.pbio.1000588
    • Navarro MVAS, et al. 2011. Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis. PLoS Biol. 9:e1000588. doi:10.1371/journal.pbio.1000588.
    • (2011) PLoS Biol. , vol.9
    • Navarro, M.V.A.S.1
  • 29
    • 70350501347 scopus 로고    scopus 로고
    • A flavin cofactor-binding PAS domain regulates c-di-GMP synthesis in AxDGC2 from Acetobacter xyli- num
    • Qi Y, Rao F, Luo Z, Liang Z-X. 2009. A flavin cofactor-binding PAS domain regulates c-di-GMP synthesis in AxDGC2 from Acetobacter xyli- num. Biochemistry 48:10275-10285.
    • (2009) Biochemistry , vol.48 , pp. 10275-10285
    • Qi, Y.1    Rao, F.2    Luo, Z.3    Liang, Z-X.4
  • 30
    • 67349108043 scopus 로고    scopus 로고
    • Enzymatic synthesis of c-di-GMP using a thermophilic diguanylate cyclase
    • Rao F, et al. 2009. Enzymatic synthesis of c-di-GMP using a thermophilic diguanylate cyclase. Anal. Biochem. 389:138-142.
    • (2009) Anal. Biochem. , vol.389 , pp. 138-142
    • Rao, F.1
  • 31
    • 67749113278 scopus 로고    scopus 로고
    • The functional role of a conserved loop in EAL domain-based c-di-GMP specific phosphodiesterase
    • Rao F, et al. 2009. The functional role of a conserved loop in EAL domain-based c-di-GMP specific phosphodiesterase. J. Bacteriol. 191:4722-4731.
    • (2009) J. Bacteriol. , vol.191 , pp. 4722-4731
    • Rao, F.1
  • 32
    • 47049115663 scopus 로고    scopus 로고
    • Catalytic mechanism of c-di-GMP specific phosphodiesterase: a study of the EAL domain-containing RocR from Pseudomonas aeruginosa
    • Rao F, Yang Y, Qi Y, Liang ZX. 2008. Catalytic mechanism of c-di-GMP specific phosphodiesterase: a study of the EAL domain-containing RocR from Pseudomonas aeruginosa. J. Bacteriol. 190:3622-3631.
    • (2008) J. Bacteriol. , vol.190 , pp. 3622-3631
    • Rao, F.1    Yang, Y.2    Qi, Y.3    Liang, Z.X.4
  • 33
    • 0038154011 scopus 로고    scopus 로고
    • Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily
    • Robinson VL, Wu T, Stock AM. 2003. Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily. J. Bacteriol. 185:4186-4194.
    • (2003) J. Bacteriol. , vol.185 , pp. 4186-4194
    • Robinson, V.L.1    Wu, T.2    Stock, A.M.3
  • 34
    • 34248347847 scopus 로고    scopus 로고
    • Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg
    • Roessle MW, et al. 2007. Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J. Appl. Crystallogr. 40:s190-s194.
    • (2007) J. Appl. Crystallogr. , vol.40
    • Roessle, M.W.1
  • 35
    • 22644438480 scopus 로고    scopus 로고
    • C-di-GMP: the dawning of a novel bacterial signaling system
    • Romling U, Gomelsky M, Galperin MY. 2005. C-di-GMP: the dawning of a novel bacterial signaling system. Mol. Microbiol. 57:629-639.
    • (2005) Mol. Microbiol. , vol.57 , pp. 629-639
    • Romling, U.1    Gomelsky, M.2    Galperin, M.Y.3
  • 36
    • 0023090935 scopus 로고
    • Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylate
    • Ross P. 1987. Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylate. Nature 325:279-281.
    • (1987) Nature , vol.325 , pp. 279-281
    • Ross, P.1
  • 37
    • 51949084084 scopus 로고    scopus 로고
    • Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33
    • Round AR, et al. 2008. Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J. Appl. Crystallogr. 41:913-917.
    • (2008) J. Appl. Crystallogr. , vol.41 , pp. 913-917
    • Round, A.R.1
  • 38
    • 33646249963 scopus 로고    scopus 로고
    • Cell-cell signaling in Xanthomonas campestris in- volves an HD-GYP domain protein that functions in cyclic di-GMP turn- over
    • U.S.A.
    • Ryan RP, et al. 2006. Cell-cell signaling in Xanthomonas campestris in- volves an HD-GYP domain protein that functions in cyclic di-GMP turn- over. Proc. Natl. Acad. Sci. U. S. A. 103:6712-6717.
    • (2006) Proc. Natl. Acad. Sci. , vol.103 , pp. 6712-6717
    • Ryan, R.P.1
  • 39
    • 14244254898 scopus 로고    scopus 로고
    • Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain
    • Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M. 2005. Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J. Bacteriol. 187:1792-1798.
    • (2005) J. Bacteriol. , vol.187 , pp. 1792-1798
    • Ryjenkov, D.A.1    Tarutina, M.2    Moskvin, O.V.3    Gomelsky, M.4
  • 40
    • 70349274104 scopus 로고    scopus 로고
    • Structural and mechanistic determinants of c-di-GMP signaling
    • Schirmer T, Jenal U. 2009. Structural and mechanistic determinants of c-di-GMP signaling. Nat. Rev. Microbiol. 7:724-735.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 724-735
    • Schirmer, T.1    Jenal, U.2
  • 41
    • 21844451590 scopus 로고    scopus 로고
    • The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains
    • Schmidt AJ, Ryjenkov DA, Gomelsky M. 2005. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187:4774-4781.
    • (2005) J. Bacteriol. , vol.187 , pp. 4774-4781
    • Schmidt, A.J.1    Ryjenkov, D.A.2    Gomelsky, M.3
  • 43
    • 77950793231 scopus 로고    scopus 로고
    • Experimental phasing with SHELXC/D/E: combining chain tracing with density modification
    • Sheldrick G. 2010. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. Sect. D 66:479-485.
    • (2010) Acta Crystallogr. Sect. , vol.D 66 , pp. 479-485
    • Sheldrick, G.1
  • 44
    • 0026910457 scopus 로고
    • Determination of the regularization parameter in indi- rect-transform methods using perceptual criteria
    • Svergun D. 1992. Determination of the regularization parameter in indi- rect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25: 495-503.
    • (1992) J. Appl. Crystallogr. , vol.25 , pp. 495-503
    • Svergun, D.1
  • 45
    • 0029185933 scopus 로고
    • CRYSOL: a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun D, Barberato C, Koch MHJ. 1995. CRYSOL: a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28:768-773.
    • (1995) J. Appl. Crystallogr. , vol.28 , pp. 768-773
    • Svergun, D.1    Barberato, C.2    Koch, M.H.J.3
  • 46
    • 77956921553 scopus 로고    scopus 로고
    • Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases
    • Tchigvintsev A, et al. 2010. Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J. Mol. Biol. 402:524-538.
    • (2010) J. Mol. Biol. , vol.402 , pp. 524-538
    • Tchigvintsev, A.1
  • 47
    • 18144411635 scopus 로고    scopus 로고
    • Structural analysis and solution studies of the activated regulatory domain of the response regu-lator ArcA: a symmetric dimer mediated by the Universal-GreekwithMathPi.-1.H92514-Universal-GreekwithMathPi.-1.H92525-Universal-GreekwithMathPi.-1.H92515 face
    • Toro-Roman A, Mack TR, Stock AM. 2005. Structural analysis and solution studies of the activated regulatory domain of the response regu-lator ArcA: a symmetric dimer mediated by the Universal-GreekwithMathPi.-1.H92514-Universal-GreekwithMathPi.-1.H92525-Universal-GreekwithMathPi.-1.H92515 face. J. Mol. Biol. 349:11-26.
    • (2005) J. Mol. Biol. , vol.349 , pp. 11-26
    • Toro-Roman, A.1    Mack, T.R.2    Stock, A.M.3
  • 48
    • 0027366420 scopus 로고
    • Structural conservation in the CheY superfamily
    • Volz K. 1993. Structural conservation in the CheY superfamily. J. Biol. Chem. 32:11741-11753.
    • (1993) J. Biol. Chem. , vol.32 , pp. 11741-11753
    • Volz, K.1
  • 50
    • 34547659282 scopus 로고    scopus 로고
    • Structure of BeF3-modified response regula- tor PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition
    • Wassmann P, et al. 2007. Structure of BeF3-modified response regula- tor PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure 15:915-927.
    • (2007) Structure , vol.15 , pp. 915-927
    • Wassmann, P.1


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