메뉴 건너뛰기




Volumn 359, Issue 2, 2006, Pages 390-402

Structures of Ubiquitin Insertion Mutants Support Site-specific Reflex Response to Insertions Hypothesis

Author keywords

crystallography; homology modeling; indels; protein engineering; ubiquitin

Indexed keywords

AMINO ACID; UBIQUITIN;

EID: 33745556198     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.03.047     Document Type: Article
Times cited : (6)

References (40)
  • 1
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • Chimpanzee Sequencing and Analysis Consortium
    • Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
    • (2005) Nature , vol.437 , pp. 69-87
  • 3
    • 0027176364 scopus 로고
    • The relationship between trinucleotide (CAG) repeat length and clinical features of Huntington's disease
    • Andrew S.E., Goldberg Y.P., Kremer B., Telenius H., Theilmann J., Adam S., et al. The relationship between trinucleotide (CAG) repeat length and clinical features of Huntington's disease. Nature Genet. 4 (1993) 398-403
    • (1993) Nature Genet. , vol.4 , pp. 398-403
    • Andrew, S.E.1    Goldberg, Y.P.2    Kremer, B.3    Telenius, H.4    Theilmann, J.5    Adam, S.6
  • 4
    • 0038657551 scopus 로고    scopus 로고
    • Sequence-selective DNA cleavage by a chimeric metallopeptide
    • Kovacic R.T., Welch J.T., and Franklin S.J. Sequence-selective DNA cleavage by a chimeric metallopeptide. J. Am. Chem. Soc. 125 (2003) 6656-6662
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 6656-6662
    • Kovacic, R.T.1    Welch, J.T.2    Franklin, S.J.3
  • 6
    • 11144298983 scopus 로고    scopus 로고
    • De novo design of a copper(II)-binding helix-turn-telix chimera: the prion octarepeat motif in a new context
    • Shields S.B., and Franklin S.J. De novo design of a copper(II)-binding helix-turn-telix chimera: the prion octarepeat motif in a new context. Biochemistry 43 (2004) 16086-16091
    • (2004) Biochemistry , vol.43 , pp. 16086-16091
    • Shields, S.B.1    Franklin, S.J.2
  • 7
    • 0029130841 scopus 로고
    • The emerging role of insertions and deletions in protein engineering
    • Shortle D., and Sondek J. The emerging role of insertions and deletions in protein engineering. Curr. Opin. Biotechnol. 6 (1995) 387-393
    • (1995) Curr. Opin. Biotechnol. , vol.6 , pp. 387-393
    • Shortle, D.1    Sondek, J.2
  • 8
    • 0025339507 scopus 로고
    • Accomodation of single amino acid insertions by the native state of staphylococcal nuclease
    • Sondek J., and Shortle D. Accomodation of single amino acid insertions by the native state of staphylococcal nuclease. Proteins: Struct. Funct. Genet. 7 (1990) 299-305
    • (1990) Proteins: Struct. Funct. Genet. , vol.7 , pp. 299-305
    • Sondek, J.1    Shortle, D.2
  • 9
    • 0242330730 scopus 로고    scopus 로고
    • Assessment of homology-based predictions in CASP5
    • Tramontano A., and Morea V. Assessment of homology-based predictions in CASP5. Proteins: Struct. Funct. Genet. 7,53 (2003) 352-368
    • (2003) Proteins: Struct. Funct. Genet. , vol.7-53 , pp. 352-368
    • Tramontano, A.1    Morea, V.2
  • 10
    • 24044437492 scopus 로고    scopus 로고
    • Site-specific reflex response of ubiquitin to loop insertions
    • Ferraro D.M., Hope E.K., and Robertson A.D. Site-specific reflex response of ubiquitin to loop insertions. J. Mol. Biol. 352 (2005) 575-584
    • (2005) J. Mol. Biol. , vol.352 , pp. 575-584
    • Ferraro, D.M.1    Hope, E.K.2    Robertson, A.D.3
  • 11
    • 0032561784 scopus 로고    scopus 로고
    • 2H dipolar NMR study of the water molecule in crystalline hydrates
    • 2H dipolar NMR study of the water molecule in crystalline hydrates. J. Am. Chem. Soc. 120 (1998) 13187-13193
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 13187-13193
    • Wu, G.1    Freure, C.J.2    Verdurand, E.3
  • 12
    • 0037116509 scopus 로고    scopus 로고
    • An ab initio study of amide proton shift tensor dependence on local protein structure
    • Sharma Y., Kwon O.Y., Brooks B., and Tjandra N. An ab initio study of amide proton shift tensor dependence on local protein structure. J. Am. Chem. Soc. 124 (2002) 327-335
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 327-335
    • Sharma, Y.1    Kwon, O.Y.2    Brooks, B.3    Tjandra, N.4
  • 13
    • 0035167185 scopus 로고    scopus 로고
    • Crystal structure of molybdopterin synthase and its evolutionary relationship to ubquitin activation
    • Rudolph M.J., Wuebbens M.M., Rajagopalan K.V., and Schindelin H. Crystal structure of molybdopterin synthase and its evolutionary relationship to ubquitin activation. Nature Struct. Biol. 8 (2001) 42-46
    • (2001) Nature Struct. Biol. , vol.8 , pp. 42-46
    • Rudolph, M.J.1    Wuebbens, M.M.2    Rajagopalan, K.V.3    Schindelin, H.4
  • 14
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 Å resolution
    • Vijay-Kumar S., Bugg C.E., and Cook W.J. Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194 (1987) 531-544
    • (1987) J. Mol. Biol. , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 15
    • 0026746290 scopus 로고
    • Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2)
    • Cook W.J., Jeffrey L.C., Carson M., Chen Z., and Pickart C.M. Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2). J. Biol. Chem. 267 (1992) 16467-16471
    • (1992) J. Biol. Chem. , vol.267 , pp. 16467-16471
    • Cook, W.J.1    Jeffrey, L.C.2    Carson, M.3    Chen, Z.4    Pickart, C.M.5
  • 16
    • 0028316184 scopus 로고
    • Structure of tetraubiquitin shows how multiubiquitin chains can be formed
    • Cook W.J., Jeffrey L.C., Kasperek E., and Pickart C.M. Structure of tetraubiquitin shows how multiubiquitin chains can be formed. J. Mol. Biol. 236 (1994) 601-609
    • (1994) J. Mol. Biol. , vol.236 , pp. 601-609
    • Cook, W.J.1    Jeffrey, L.C.2    Kasperek, E.3    Pickart, C.M.4
  • 17
    • 0037184947 scopus 로고    scopus 로고
    • Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde
    • Hu M., Li P., Li M., Li W., Yao T., Wu J.W., et al. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell 111 (2002) 1041-1054
    • (2002) Cell , vol.111 , pp. 1041-1054
    • Hu, M.1    Li, P.2    Li, M.3    Li, W.4    Yao, T.5    Wu, J.W.6
  • 18
    • 0033565867 scopus 로고    scopus 로고
    • Structural basis for the specificity of ubiquitin C-terminal hydrolases
    • Johnston S.C., Riddle S.M., Cohen R.E., and Hill C.P. Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J. 18 (1999) 3877-3887
    • (1999) EMBO J. , vol.18 , pp. 3877-3887
    • Johnston, S.C.1    Riddle, S.M.2    Cohen, R.E.3    Hill, C.P.4
  • 21
    • 0028268603 scopus 로고
    • Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin
    • Ramage R., Green J., Muir T.W., Ogunjobi O.M., Love S., and Shaw K. Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin. Biochem. J. 299 (1994) 151-158
    • (1994) Biochem. J. , vol.299 , pp. 151-158
    • Ramage, R.1    Green, J.2    Muir, T.W.3    Ogunjobi, O.M.4    Love, S.5    Shaw, K.6
  • 22
    • 3142758686 scopus 로고    scopus 로고
    • Automated protein structure homology modeling: a progress report
    • Kopp J., and Schwede T. Automated protein structure homology modeling: a progress report. Pharmacogenomics 5 (2004) 405-416
    • (2004) Pharmacogenomics , vol.5 , pp. 405-416
    • Kopp, J.1    Schwede, T.2
  • 23
    • 17744387920 scopus 로고    scopus 로고
    • All are not equal: a benchmark of different homology modeling programs
    • Wallner B., and Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci. 14 (2005) 1315-1327
    • (2005) Protein Sci. , vol.14 , pp. 1315-1327
    • Wallner, B.1    Elofsson, A.2
  • 24
    • 0032900490 scopus 로고    scopus 로고
    • NMR screening in drug discovery
    • Moore J.M. NMR screening in drug discovery. Curr. Opin. Biotechnol. 10 (1999) 54-58
    • (1999) Curr. Opin. Biotechnol. , vol.10 , pp. 54-58
    • Moore, J.M.1
  • 27
    • 0032555125 scopus 로고    scopus 로고
    • Effect of an amino acid insertion into the omega loop region of a class C β-lactamase on its substrate specificity
    • Nukaga M., Taniguchi K., Washio Y., and Sawai T. Effect of an amino acid insertion into the omega loop region of a class C β-lactamase on its substrate specificity. Biochemistry 37 (1998) 10461-10468
    • (1998) Biochemistry , vol.37 , pp. 10461-10468
    • Nukaga, M.1    Taniguchi, K.2    Washio, Y.3    Sawai, T.4
  • 28
    • 13244289775 scopus 로고    scopus 로고
    • Sequence swapping does not result in conformation swapping for the β4/β5 and β8/β9 β-hairpin turns in human acidic fibroblast growth factor
    • Kim J., Lee J., Brych S.R., Logan T.M., and Blaber M. Sequence swapping does not result in conformation swapping for the β4/β5 and β8/β9 β-hairpin turns in human acidic fibroblast growth factor. Protein Sci. 14 (2005) 351-359
    • (2005) Protein Sci. , vol.14 , pp. 351-359
    • Kim, J.1    Lee, J.2    Brych, S.R.3    Logan, T.M.4    Blaber, M.5
  • 29
    • 0033213239 scopus 로고    scopus 로고
    • The finer things in X-ray diffraction data collection
    • Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallog. sect. D 55 (1999) 1718-1725
    • (1999) Acta Crystallog. sect. D , vol.55 , pp. 1718-1725
    • Pflugrath, J.W.1
  • 30
    • 0027879008 scopus 로고
    • Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
    • Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallog. 26 (1993) 795-800
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 795-800
    • Kabsch, W.1
  • 32
    • 84920325457 scopus 로고
    • AMoRe: an automated package for molecular replacement
    • Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A 50 (1994) 157-163
    • (1994) Acta Crystallog. sect. A , vol.50 , pp. 157-163
    • Navaza, J.1
  • 33
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 34
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
    • (1991) Acta Crystallog. sect. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard4
  • 35
    • 84901961522 scopus 로고
    • Slow-cooling protocols for crystallographic refinement by simulated annealing
    • Brunger A.T., Krukowski A., and Erickson J.W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog. sect. A 46 (1990) 585-593
    • (1990) Acta Crystallog. sect. A , vol.46 , pp. 585-593
    • Brunger, A.T.1    Krukowski, A.2    Erickson, J.W.3
  • 38
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density
    • McRee D.E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 39
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect. D 60 (2004) 2126-2132
    • (2004) Acta Crystallog. sect. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.