메뉴 건너뛰기




Volumn 105, Issue 7, 2008, Pages 2343-2348

Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds

Author keywords

Conformational switching; Structural evolution; Transitive homology; X ray crystallography

Indexed keywords

DNA BINDING PROTEIN; PROTEIN PFL 6; PROTEIN XFASO 1; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; REPRESSOR PROTEIN; VIRUS PROTEIN;

EID: 40649108103     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711589105     Document Type: Article
Times cited : (76)

References (49)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 0141634362 scopus 로고    scopus 로고
    • Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    • Sadreyev RI, Baker D, Grishin NV (2003) Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci 12:2262-2272.
    • (2003) Protein Sci , vol.12 , pp. 2262-2272
    • Sadreyev, R.I.1    Baker, D.2    Grishin, N.V.3
  • 3
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244-W248.
    • (2005) Nucleic Acids Res , vol.33
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 5
    • 0031762837 scopus 로고    scopus 로고
    • Measurement of the effectiveness of transitive sequence comparison, through a third "intermediate" sequence
    • Gerstein M (1998) Measurement of the effectiveness of transitive sequence comparison, through a third "intermediate" sequence. Bioinformatics 14:707-714.
    • (1998) Bioinformatics , vol.14 , pp. 707-714
    • Gerstein, M.1
  • 6
    • 0034491129 scopus 로고    scopus 로고
    • Saturated BLAST: An automated multiple intermediate sequence search used to detect distant homology
    • Li W, Pio F, Pawlowski K, Godzik A (2000) Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 16:1105-1110.
    • (2000) Bioinformatics , vol.16 , pp. 1105-1110
    • Li, W.1    Pio, F.2    Pawlowski, K.3    Godzik, A.4
  • 7
    • 0032940341 scopus 로고    scopus 로고
    • Combining sensitive database searches with multiple intermediates to detect distant homologues
    • Salamov AA, Suwa M, Orengo CA, Swindells MB (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng 12:95-100.
    • (1999) Protein Eng , vol.12 , pp. 95-100
    • Salamov, A.A.1    Suwa, M.2    Orengo, C.A.3    Swindells, M.B.4
  • 8
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park J, Teichmann SA, Hubbard T, Chothia C (1997) Intermediate sequences increase the detection of homology between sequences. J Mol Biol 273:349-354.
    • (1997) J Mol Biol , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.A.2    Hubbard, T.3    Chothia, C.4
  • 9
    • 33749262632 scopus 로고    scopus 로고
    • Common evolutionary origin of swapped-hairpin and double-psi beta barrels
    • Coles M, et al. (2006) Common evolutionary origin of swapped-hairpin and double-psi beta barrels. Structure (London) 14:1489-1498.
    • (2006) Structure (London) , vol.14 , pp. 1489-1498
    • Coles, M.1
  • 11
    • 0033754089 scopus 로고    scopus 로고
    • Sequence of the genome of Salmonella bacteriophage P22
    • Vander Byl C, Kropinski AM (2000) Sequence of the genome of Salmonella bacteriophage P22. J Bacteriol 182:6472-6481.
    • (2000) J Bacteriol , vol.182 , pp. 6472-6481
    • Vander Byl, C.1    Kropinski, A.M.2
  • 12
    • 0037312792 scopus 로고    scopus 로고
    • Corrected sequence of the bacteriophage p22 genome
    • Pedulla ML, et al. (2003) Corrected sequence of the bacteriophage p22 genome. J Bacteriol 185:1475-1477.
    • (2003) J Bacteriol , vol.185 , pp. 1475-1477
    • Pedulla, M.L.1
  • 14
    • 0007208716 scopus 로고
    • Interactions between DNA-bound repressors govern regulation by the lambda phage repressor
    • Johnson AD, Meyer BJ, Ptashne M (1979) Interactions between DNA-bound repressors govern regulation by the lambda phage repressor. Proc Natl Acad Sci USA 76:5061-5065.
    • (1979) Proc Natl Acad Sci USA , vol.76 , pp. 5061-5065
    • Johnson, A.D.1    Meyer, B.J.2    Ptashne, M.3
  • 15
    • 0018880549 scopus 로고
    • Bacteriophage lambda repressor and cro protein: Interactions with operator DNA
    • Johnson AD, Pabo CO, Sauer RT (1980) Bacteriophage lambda repressor and cro protein: Interactions with operator DNA. Methods Enzymol 65:839-856.
    • (1980) Methods Enzymol , vol.65 , pp. 839-856
    • Johnson, A.D.1    Pabo, C.O.2    Sauer, R.T.3
  • 16
    • 0023048289 scopus 로고
    • Bacteriophage P22 Cro protein: Sequence, purification, and properties
    • Poteete AR, Hehir K, Sauer RT (1986) Bacteriophage P22 Cro protein: Sequence, purification, and properties. Biochemistry 25:251-256.
    • (1986) Biochemistry , vol.25 , pp. 251-256
    • Poteete, A.R.1    Hehir, K.2    Sauer, R.T.3
  • 17
    • 0032479329 scopus 로고    scopus 로고
    • Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution
    • Albright RA, Matthews BW (1998) Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution. J Mol Biol 280:137-151.
    • (1998) J Mol Biol , vol.280 , pp. 137-151
    • Albright, R.A.1    Matthews, B.W.2
  • 18
    • 0032479285 scopus 로고    scopus 로고
    • Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity
    • Ohlendorf DH, Tronrud DE, Matthews BW (1998) Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity. J Mol Biol 280:129-136.
    • (1998) J Mol Biol , vol.280 , pp. 129-136
    • Ohlendorf, D.H.1    Tronrud, D.E.2    Matthews, B.W.3
  • 19
    • 0037418253 scopus 로고    scopus 로고
    • Retroevolution of lambda Cro toward a stable monomer
    • LeFevre KR, Cordes MH (2003) Retroevolution of lambda Cro toward a stable monomer. Proc Natl Acad Sci USA 100:2345-2350.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 2345-2350
    • LeFevre, K.R.1    Cordes, M.H.2
  • 20
    • 21744443969 scopus 로고    scopus 로고
    • Slow assembly and disassembly of lambda Cro repressor dimers
    • Jia H, Satumba WJ, Bidwell GL, III, Mossing MC (2005) Slow assembly and disassembly of lambda Cro repressor dimers. J Mol Biol 350:919-929.
    • (2005) J Mol Biol , vol.350 , pp. 919-929
    • Jia, H.1    Satumba, W.J.2    Bidwell III, G.L.3    Mossing, M.C.4
  • 21
    • 0034687127 scopus 로고    scopus 로고
    • Coupled energetics of lambda cro repressor self-assembly and site- specific DNA operator binding I: Analysis of cro dimerization from nanomolar to micromolar concentrations
    • Darling PJ, Holt JM, Ackers GK (2000) Coupled energetics of lambda cro repressor self-assembly and site- specific DNA operator binding I: Analysis of cro dimerization from nanomolar to micromolar concentrations. Biochemistry 39:11500-11507.
    • (2000) Biochemistry , vol.39 , pp. 11500-11507
    • Darling, P.J.1    Holt, J.M.2    Ackers, G.K.3
  • 22
    • 33744783371 scopus 로고    scopus 로고
    • Evolution of protein fold in the presence of functional constraints
    • Andreeva A, Murzin AG (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16:399-408.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 399-408
    • Andreeva, A.1    Murzin, A.G.2
  • 23
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin NV (2001) Fold change in evolution of protein structures. J Struct Biol 134:167-185.
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 24
    • 0344642994 scopus 로고    scopus 로고
    • Homologous proteins with different folds: The three-dimensional structures of domains 1 and 6 of the multiple Kazal-type inhibitor LEKTI
    • Lauber T, Schulz A, Schweimer K, Adermann K, Marx UC (2003) Homologous proteins with different folds: The three-dimensional structures of domains 1 and 6 of the multiple Kazal-type inhibitor LEKTI. J Mol Biol 328:205-219.
    • (2003) J Mol Biol , vol.328 , pp. 205-219
    • Lauber, T.1    Schulz, A.2    Schweimer, K.3    Adermann, K.4    Marx, U.C.5
  • 25
    • 34147155174 scopus 로고    scopus 로고
    • Structural basis for converting a general transcription factor into an operon-specific virulence regulator
    • Belogurov GA, et al. (2007) Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell 26:117-129.
    • (2007) Mol Cell , vol.26 , pp. 117-129
    • Belogurov, G.A.1
  • 26
    • 33646864516 scopus 로고    scopus 로고
    • A trade between similar but nonequivalent intrasubunit and intersubunit contacts in Cro dimer evolution
    • Newlove T, Atkinson KR, Van Dorn LO, Cordes MH (2006) A trade between similar but nonequivalent intrasubunit and intersubunit contacts in Cro dimer evolution. Biochemistry 45:6379-6391.
    • (2006) Biochemistry , vol.45 , pp. 6379-6391
    • Newlove, T.1    Atkinson, K.R.2    Van Dorn, L.O.3    Cordes, M.H.4
  • 27
    • 0033514996 scopus 로고    scopus 로고
    • Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage
    • Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 96:2192-2197.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 2192-2197
    • Hendrix, R.W.1    Smith, M.C.2    Burns, R.N.3    Ford, M.E.4    Hatfull, G.F.5
  • 28
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47:3-8.
    • (1998) Syst Biol , vol.47 , pp. 3-8
    • Hillis, D.M.1
  • 29
    • 0033555717 scopus 로고    scopus 로고
    • Exploring the conformational properties of the sequence space between two proteins with different folds: An experimental study
    • Blanco FJ, Angrand I, Serrano L (1999) Exploring the conformational properties of the sequence space between two proteins with different folds: an experimental study. J Mol Biol 285:741-753.
    • (1999) J Mol Biol , vol.285 , pp. 741-753
    • Blanco, F.J.1    Angrand, I.2    Serrano, L.3
  • 30
    • 33748269731 scopus 로고    scopus 로고
    • Relationship between the sequence determinants of stability for two natural homologous proteins with different folds
    • Van Dorn LO, Newlove T, Chang S, Ingram WM, Cordes MH (2006) Relationship between the sequence determinants of stability for two natural homologous proteins with different folds. Biochemistry 45:10542-10553.
    • (2006) Biochemistry , vol.45 , pp. 10542-10553
    • Van Dorn, L.O.1    Newlove, T.2    Chang, S.3    Ingram, W.M.4    Cordes, M.H.5
  • 31
    • 0028871804 scopus 로고
    • How to measure and predict the molar absorption coefficient of a protein
    • Pace CN, Vajdos F, Fee L, Grimsley G, Gray T (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci 4:2411-2423.
    • (1995) Protein Sci , vol.4 , pp. 2411-2423
    • Pace, C.N.1    Vajdos, F.2    Fee, L.3    Grimsley, G.4    Gray, T.5
  • 32
    • 0014109212 scopus 로고
    • Spectroscopic determination of tryptophan and tyrosine in proteins
    • Edelhoch H (1967) Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6:1948-1954.
    • (1967) Biochemistry , vol.6 , pp. 1948-1954
    • Edelhoch, H.1
  • 33
    • 0027439390 scopus 로고
    • Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
    • Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol 229:105-124.
    • (1993) J Mol Biol , vol.229 , pp. 105-124
    • Van Duyne, G.D.1    Standaert, R.F.2    Karplus, P.A.3    Schreiber, S.L.4    Clardy, J.5
  • 34
    • 0033213239 scopus 로고    scopus 로고
    • The finer things in x-ray diffraction data collection
    • Pflugrath JW (1999) The finer things in x-ray diffraction data collection. Acta Crystallogr D 55:1718-1725.
    • (1999) Acta Crystallogr D , vol.55 , pp. 1718-1725
    • Pflugrath, J.W.1
  • 35
    • 0033831935 scopus 로고    scopus 로고
    • A flexible and efficient procedure for the solution and phase refinement of protein structures
    • Foadi J, et al. (2000) A flexible and efficient procedure for the solution and phase refinement of protein structures. Acta Crystallogr D 56:1137-1147.
    • (2000) Acta Crystallogr D , vol.56 , pp. 1137-1147
    • Foadi, J.1
  • 36
    • 42049109413 scopus 로고    scopus 로고
    • Cowtan K (1994) dm: An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31:34-38.
    • Cowtan K (1994) "dm": An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31:34-38.
  • 37
    • 2142689200 scopus 로고    scopus 로고
    • SOLVE and RESOLVE: Automated structure solution, density modification and model building
    • Terwilliger T (2004) SOLVE and RESOLVE: Automated structure solution, density modification and model building. J Synchrotron Radiat 11:49-52.
    • (2004) J Synchrotron Radiat , vol.11 , pp. 49-52
    • Terwilliger, T.1
  • 38
    • 0032964481 scopus 로고    scopus 로고
    • Automated protein model building combined with iterative structure refinement
    • Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6:458-463.
    • (1999) Nat Struct Biol , vol.6 , pp. 458-463
    • Perrakis, A.1    Morris, R.2    Lamzin, V.S.3
  • 39
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132.
    • (2004) Acta Crystallogr D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 40
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin AA, Teplyakov A (1997) MOLREP: An automated program for molecular replacement. J Appl Crystallogr 30:1022-1025.
    • (1997) J Appl Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.A.1    Teplyakov, A.2
  • 41
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53:240-255.
    • (1997) Acta Crystallogr D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 42
    • 0028103275 scopus 로고    scopus 로고
    • Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
    • Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
  • 44
    • 0033896691 scopus 로고    scopus 로고
    • Maximum-likelihood density modification
    • Terwilliger TC (2000) Maximum-likelihood density modification. Acta Crystallogr D 56:965-972.
    • (2000) Acta Crystallogr D , vol.56 , pp. 965-972
    • Terwilliger, T.C.1
  • 45
    • 0347383761 scopus 로고    scopus 로고
    • SOLVE and RESOLVE: Automated structure solution and density modification
    • Terwilliger TC (2003) SOLVE and RESOLVE: Automated structure solution and density modification. Methods Enzymol 374:22-37.
    • (2003) Methods Enzymol , vol.374 , pp. 22-37
    • Terwilliger, T.C.1
  • 46
    • 33645158291 scopus 로고    scopus 로고
    • TLSMD web server for the generation of multi-group TLS models
    • Painter J, Merritt EA (2006) TLSMD web server for the generation of multi-group TLS models. J Appl Crystallogr 39:109-111.
    • (2006) J Appl Crystallogr , vol.39 , pp. 109-111
    • Painter, J.1    Merritt, E.A.2
  • 47
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    • Painter J, Merritt EA (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D 62:439-450.
    • (2006) Acta Crystallogr D , vol.62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 49
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
    • (1991) J Appl Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.