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Volumn 343, Issue 4, 2004, Pages 971-984

The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution

Author keywords

calcium; EF hand; evolution; protein structure; structure motifs

Indexed keywords

ANTIGEN; CALCIUM; CALCIUM BINDING PROTEIN; PROTEIN; THROMBOSPONDIN;

EID: 5144226338     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.08.077     Document Type: Article
Times cited : (110)

References (69)
  • 3
    • 0037022309 scopus 로고    scopus 로고
    • Calcium signaling: A tale for all seasons
    • E. Carafoli Calcium signaling: a tale for all seasons Proc. Natl Acad. Sci. USA 99 2002 1115 1122
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 1115-1122
    • Carafoli, E.1
  • 4
    • 0026409654 scopus 로고
    • Calcium-binding sites in proteins: A structural perspective
    • C.A. McPhalen, N.C. Strynadka, and M.N. James Calcium-binding sites in proteins: a structural perspective Advan. Protein Chem. 42 1991 77 144
    • (1991) Advan. Protein Chem. , vol.42 , pp. 77-144
    • McPhalen, C.A.1    Strynadka, N.C.2    James, M.N.3
  • 5
    • 0027292152 scopus 로고
    • Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: A two-domain protein with a calcium binding parallel beta roll motif
    • U. Baumann, S. Wu, K.M. Flaherty, and D.B. McKay Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif EMBO J. 12 1993 3357 3364
    • (1993) EMBO J. , vol.12 , pp. 3357-3364
    • Baumann, U.1    Wu, S.2    Flaherty, K.M.3    McKay, D.B.4
  • 7
    • 0024396312 scopus 로고
    • Crystal structures of the helix-loop-helix calcium-binding proteins
    • N.C. Strynadka, and M.N. James Crystal structures of the helix-loop-helix calcium-binding proteins Annu. Rev. Biochem. 58 1989 951 998
    • (1989) Annu. Rev. Biochem. , vol.58 , pp. 951-998
    • Strynadka, N.C.1    James, M.N.2
  • 9
    • 0032454584 scopus 로고    scopus 로고
    • Classification and evolution of EF-hand proteins
    • H. Kawasaki, S. Nakayama, and R.H. Kretsinger Classification and evolution of EF-hand proteins Biometals 11 1998 277 295
    • (1998) Biometals , vol.11 , pp. 277-295
    • Kawasaki, H.1    Nakayama, S.2    Kretsinger, R.H.3
  • 11
    • 0033567217 scopus 로고    scopus 로고
    • About the role of conserved amino acid residues in the calcium-binding site of proteins
    • B. Dragani, and A. Aceto About the role of conserved amino acid residues in the calcium-binding site of proteins Arch. Biochem. Biophys. 368 1999 211 213
    • (1999) Arch. Biochem. Biophys. , vol.368 , pp. 211-213
    • Dragani, B.1    Aceto, A.2
  • 14
    • 0023256886 scopus 로고
    • A novel calcium binding site in the galactose-binding protein of bacterial transport and chemotaxis
    • N.K. Vyas, M.N. Vyas, and F.A. Quiocho A novel calcium binding site in the galactose-binding protein of bacterial transport and chemotaxis Nature 327 1987 635 638
    • (1987) Nature , vol.327 , pp. 635-638
    • Vyas, N.K.1    Vyas, M.N.2    Quiocho, F.A.3
  • 15
    • 0027340581 scopus 로고
    • The 1.7 Å refined X-ray structure of the periplasmic glucose/galactose receptor from Salmonella typhimurium
    • J.Y. Zou, M.M. Flocco, and S.L. Mowbray The 1.7 Å refined X-ray structure of the periplasmic glucose/galactose receptor from Salmonella typhimurium J. Mol. Biol. 233 1993 739 752
    • (1993) J. Mol. Biol. , vol.233 , pp. 739-752
    • Zou, J.Y.1    Flocco, M.M.2    Mowbray, S.L.3
  • 16
    • 0035970297 scopus 로고    scopus 로고
    • Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain
    • B.L. Lytle, B.F. Volkman, W.M. Westler, M.P. Heckman, and J.H. Wu Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain J. Mol. Biol. 307 2001 745 753
    • (2001) J. Mol. Biol. , vol.307 , pp. 745-753
    • Lytle, B.L.1    Volkman, B.F.2    Westler, W.M.3    Heckman, M.P.4    Wu, J.H.5
  • 17
    • 0035711534 scopus 로고    scopus 로고
    • Metal binding affinity and structural properties of an isolated EF-loop in a scaffold protein
    • Y. Ye, H.W. Lee, W. Yang, S.J. Shealy, A.L. Wilkins, and Z.R. Liu Metal binding affinity and structural properties of an isolated EF-loop in a scaffold protein Protein Eng. 14 2001 1001 1013
    • (2001) Protein Eng. , vol.14 , pp. 1001-1013
    • Ye, Y.1    Lee, H.W.2    Yang, W.3    Shealy, S.J.4    Wilkins, A.L.5    Liu, Z.R.6
  • 18
    • 0042767564 scopus 로고    scopus 로고
    • A grafting approach to obtain site-specific metal-binding properties of EF-hand proteins
    • Y. Ye, S. Shealy, H.W. Lee, I. Torshin, R. Harrison, and J.J. Yang A grafting approach to obtain site-specific metal-binding properties of EF-hand proteins Protein Eng. 16 2003 429 434
    • (2003) Protein Eng. , vol.16 , pp. 429-434
    • Ye, Y.1    Shealy, S.2    Lee, H.W.3    Torshin, I.4    Harrison, R.5    Yang, J.J.6
  • 19
    • 0037432703 scopus 로고    scopus 로고
    • An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands
    • D.J. Rigden, M.J. Jedrzejas, and M.Y. Galperin An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands FEMS Microbiol. Letters 221 2003 103 110
    • (2003) FEMS Microbiol. Letters , vol.221 , pp. 103-110
    • Rigden, D.J.1    Jedrzejas, M.J.2    Galperin, M.Y.3
  • 21
    • 0142011998 scopus 로고    scopus 로고
    • Structural diversity of calcium-binding proteins in bacteria: Single-handed EF-hands?
    • D.J. Rigden, M.J. Jedrzejas, O.V. Moroz, and M.Y. Galperin Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands? Trends Microbiol. 11 2003 295 297
    • (2003) Trends Microbiol. , vol.11 , pp. 295-297
    • Rigden, D.J.1    Jedrzejas, M.J.2    Moroz, O.V.3    Galperin, M.Y.4
  • 22
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • G.J. Kleywegt Recognition of spatial motifs in protein structures J. Mol. Biol. 285 1999 1887 1897
    • (1999) J. Mol. Biol. , vol.285 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 23
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in non-homologous tertiary structures
    • A. Stark, and R.B. Russell Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures Nucl. Acids Res. 31 2003 3341 3344
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 24
    • 0016783764 scopus 로고
    • The calcium and magnesium binding sites on troponin and their role in the regulation of myofibrillar adenosine triphosphatase
    • J.D. Potter, and J. Gergely The calcium and magnesium binding sites on troponin and their role in the regulation of myofibrillar adenosine triphosphatase J. Biol. Chem. 250 1975 4628 4633
    • (1975) J. Biol. Chem. , vol.250 , pp. 4628-4633
    • Potter, J.D.1    Gergely, J.2
  • 25
    • 0036304144 scopus 로고    scopus 로고
    • Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0 Å resolution
    • K. Momma, B. Mikami, Y. Mishima, W. Hashimoto, and K. Murata Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0 Å resolution J. Mol. Biol. 316 2002 1051 1059
    • (2002) J. Mol. Biol. , vol.316 , pp. 1051-1059
    • Momma, K.1    Mikami, B.2    Mishima, Y.3    Hashimoto, W.4    Murata, K.5
  • 27
    • 0036354161 scopus 로고    scopus 로고
    • Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: Implications for substrate specificity and catalysis
    • A. Roujeinikova, C. Raasch, S. Sedelnikova, W. Liebl, and D.W. Rice Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis J. Mol. Biol. 321 2002 149 162
    • (2002) J. Mol. Biol. , vol.321 , pp. 149-162
    • Roujeinikova, A.1    Raasch, C.2    Sedelnikova, S.3    Liebl, W.4    Rice, D.W.5
  • 28
    • 0023661282 scopus 로고
    • Three dimensional structure of porcine pancreatic alpha-amylase at 2.9 Å resolution. Role of calcium in structure and activity
    • G. Buisson, E. Duee, R. Haser, and F. Payan Three dimensional structure of porcine pancreatic alpha-amylase at 2.9 Å resolution. Role of calcium in structure and activity EMBO J. 6 1987 3909 3916
    • (1987) EMBO J. , vol.6 , pp. 3909-3916
    • Buisson, G.1    Duee, E.2    Haser, R.3    Payan, F.4
  • 29
    • 1942535754 scopus 로고    scopus 로고
    • Structure of a thrombospondin C-terminal fragment reveals a novel calcium core in the type 3 repeats
    • M. Kvansakul, J.C. Adams, and E. Hohenester Structure of a thrombospondin C-terminal fragment reveals a novel calcium core in the type 3 repeats EMBO J. 23 2004 1223 1233
    • (2004) EMBO J. , vol.23 , pp. 1223-1233
    • Kvansakul, M.1    Adams, J.C.2    Hohenester, E.3
  • 31
    • 1342304083 scopus 로고    scopus 로고
    • Structural basis for the coordinated regulation of transglutaminase 3 by guanine nucleotides and calcium/magnesium
    • B. Ahvazi, K.M. Boeshans, W. Idler, U. Baxa, P.M. Steinert, and F. Rastinejad Structural basis for the coordinated regulation of transglutaminase 3 by guanine nucleotides and calcium/magnesium J. Biol. Chem. 279 2004 7180 7192
    • (2004) J. Biol. Chem. , vol.279 , pp. 7180-7192
    • Ahvazi, B.1    Boeshans, K.M.2    Idler, W.3    Baxa, U.4    Steinert, P.M.5    Rastinejad, F.6
  • 32
    • 0033912163 scopus 로고    scopus 로고
    • Phytochelatins and their roles in heavy metal detoxification
    • C.S. Cobbett Phytochelatins and their roles in heavy metal detoxification Plant Physiol. 123 2000 825 832
    • (2000) Plant Physiol. , vol.123 , pp. 825-832
    • Cobbett, C.S.1
  • 34
    • 0037125126 scopus 로고    scopus 로고
    • The 1.62 Å structure of Thermoascus aurantiacus endoglucanase: Completing the structural picture of subfamilies in glycoside hydrolase family 5
    • L. Lo Leggio, and S. Larsen The 1.62 Å structure of Thermoascus aurantiacus endoglucanase: completing the structural picture of subfamilies in glycoside hydrolase family 5 FEBS Letters 523 2002 103 108
    • (2002) FEBS Letters , vol.523 , pp. 103-108
    • Lo Leggio, L.1    Larsen, S.2
  • 35
    • 0342901668 scopus 로고    scopus 로고
    • Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand
    • E.J. van Asselt, A.J. Dijkstra, K.H. Kalk, B. Takacs, W. Keck, and B.W. Dijkstra Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand Struct. Fold. Des. 7 1999 1167 1180
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1167-1180
    • Van Asselt, E.J.1    Dijkstra, A.J.2    Kalk, K.H.3    Takacs, B.4    Keck, W.5    Dijkstra, B.W.6
  • 36
    • 3242887525 scopus 로고    scopus 로고
    • STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins
    • M. Heinig, and D. Frishman STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins Nucl. Acids Res. 32 2004 W500 W502
    • (2004) Nucl. Acids Res. , vol.32
    • Heinig, M.1    Frishman, D.2
  • 37
    • 0034257929 scopus 로고    scopus 로고
    • 2+-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
    • 2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity J. Mol. Biol. 301 2000 1237 1256
    • (2000) J. Mol. Biol. , vol.301 , pp. 1237-1256
    • Wilson, M.A.1    Brunger, A.T.2
  • 39
    • 3242775493 scopus 로고    scopus 로고
    • The PA14 domain, a conserved all-β domain in bacterial toxins, enzymes, adhesins and signaling molecules
    • D.J. Rigden, L.V. Mello, and M.Y. Galperin The PA14 domain, a conserved all-β domain in bacterial toxins, enzymes, adhesins and signaling molecules Trends Biochem. Sci. 29 2004 335 339
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 335-339
    • Rigden, D.J.1    Mello, L.V.2    Galperin, M.Y.3
  • 40
    • 0037375799 scopus 로고    scopus 로고
    • Efficient identification of side-chain patterns using a multidimensional index tree
    • T. Hamelryck Efficient identification of side-chain patterns using a multidimensional index tree Proteins: Struct. Funct. Genet. 51 2003 96 108
    • (2003) Proteins: Struct. Funct. Genet. , vol.51 , pp. 96-108
    • Hamelryck, T.1
  • 41
    • 0029865623 scopus 로고    scopus 로고
    • Context-dependent secondary structure formation of a designed protein sequence
    • D.L. Minor Jr, and P.S. Kim Context-dependent secondary structure formation of a designed protein sequence Nature 380 1996 730 734
    • (1996) Nature , vol.380 , pp. 730-734
    • Minor Jr., D.L.1    Kim, P.S.2
  • 42
    • 0031871068 scopus 로고    scopus 로고
    • Chameleon sequences in the PDB
    • M. Mezei Chameleon sequences in the PDB Protein Eng. 11 1998 411 414
    • (1998) Protein Eng. , vol.11 , pp. 411-414
    • Mezei, M.1
  • 43
    • 0036882395 scopus 로고    scopus 로고
    • Serpin structure, mechanism, and function
    • P.G. Gettins Serpin structure, mechanism, and function Chem. Rev. 102 2002 4751 4804
    • (2002) Chem. Rev. , vol.102 , pp. 4751-4804
    • Gettins, P.G.1
  • 44
    • 0036893073 scopus 로고    scopus 로고
    • Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship
    • A.G. de Brevern, H. Valadie, S. Hazout, and C. Etchebest Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship Protein Sci. 11 2002 2871 2886
    • (2002) Protein Sci. , vol.11 , pp. 2871-2886
    • De Brevern, A.G.1    Valadie, H.2    Hazout, S.3    Etchebest, C.4
  • 45
    • 0037818341 scopus 로고    scopus 로고
    • Local structure prediction with local structure-based sequence profiles
    • A.S. Yang, and L.Y. Wang Local structure prediction with local structure-based sequence profiles Bioinformatics 19 2003 1267 1274
    • (2003) Bioinformatics , vol.19 , pp. 1267-1274
    • Yang, A.S.1    Wang, L.Y.2
  • 47
    • 0033574502 scopus 로고    scopus 로고
    • Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 Å resolution
    • S. Kamitori, S. Kondo, K. Okuyama, T. Yokota, Y. Shimura, T. Tonozuka, and Y. Sakano Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 Å resolution J. Mol. Biol. 287 1999 907 921
    • (1999) J. Mol. Biol. , vol.287 , pp. 907-921
    • Kamitori, S.1    Kondo, S.2    Okuyama, K.3    Yokota, T.4    Shimura, Y.5    Tonozuka, T.6    Sakano, Y.7
  • 48
    • 0030835856 scopus 로고    scopus 로고
    • Structure of rabbit muscle phosphoglucomutase refined at 2.4 angstrom resolution
    • Y.W. Liu, W.J. Ray, and S. Baranidharan Structure of rabbit muscle phosphoglucomutase refined at 2.4 angstrom resolution Acta Crystallog. sect. D 53 1997 392 405
    • (1997) Acta Crystallog. Sect. D , vol.53 , pp. 392-405
    • Liu, Y.W.1    Ray, W.J.2    Baranidharan, S.3
  • 49
    • 2942620151 scopus 로고    scopus 로고
    • A novel "clip-and-link" activity of repeat in toxin (RTX) proteins from gram-negative pathogens: Covalent protein cross-linking by an Asp-Lys isopeptide bond upon calcium-dependent processing at an Asp-Pro bond
    • R. Osicka, K. Prochazkova, M. Sulc, I.I. Linhartova, V. Havlicek, and P. Sebo A novel "clip-and-link" activity of repeat in toxin (RTX) proteins from gram-negative pathogens: covalent protein cross-linking by an Asp-Lys isopeptide bond upon calcium-dependent processing at an Asp-Pro bond J. Biol. Chem. 279 2004 24944 24956
    • (2004) J. Biol. Chem. , vol.279 , pp. 24944-24956
    • Osicka, R.1    Prochazkova, K.2    Sulc, M.3    Linhartova, I.I.4    Havlicek, V.5    Sebo, P.6
  • 50
    • 0031577466 scopus 로고    scopus 로고
    • A protein with a novel calcium-binding domain associated with calcareous corpuscles in Echinococcus granulosus
    • J.J. Rodrigues, H.B. Ferreira, S.E. Farias, and A. Zaha A protein with a novel calcium-binding domain associated with calcareous corpuscles in Echinococcus granulosus Biochem. Biophys. Res. Commun. 237 1997 451 456
    • (1997) Biochem. Biophys. Res. Commun. , vol.237 , pp. 451-456
    • Rodrigues, J.J.1    Ferreira, H.B.2    Farias, S.E.3    Zaha, A.4
  • 52
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • T.A. Jones, J.Y. Zou, S.W. Cowan, and M. 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    Kjeldgaard, M.4
  • 58
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • I.N. Shindyalov, and P.E. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 11 1998 739 747
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 59
    • 0031865006 scopus 로고    scopus 로고
    • Touring protein fold space with Dali/FSSP
    • L. Holm, and C. Sander Touring protein fold space with Dali/FSSP Nucl. Acids Res. 26 1998 316 319
    • (1998) Nucl. Acids Res. , vol.26 , pp. 316-319
    • Holm, L.1    Sander, C.2
  • 60
    • 0030501419 scopus 로고    scopus 로고
    • Use of non-crystallographic symmetry in protein structure refinement
    • G.J. Kleywegt Use of non-crystallographic symmetry in protein structure refinement Acta Crystallog. sect. D 52 1996 842 857
    • (1996) Acta Crystallog. Sect. D , vol.52 , pp. 842-857
    • Kleywegt, G.J.1
  • 61
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 64
    • 0032983595 scopus 로고    scopus 로고
    • Functional roles of S100 proteins, calcium-binding proteins of the EF-hand type
    • R. Donato Functional roles of S100 proteins, calcium-binding proteins of the EF-hand type Biochim. Biophys. Acta 1450 1999 191 231
    • (1999) Biochim. Biophys. Acta , vol.1450 , pp. 191-231
    • Donato, R.1
  • 65
    • 0027212083 scopus 로고
    • Spatial calcium buffering in saccular hair cells
    • W.M. Roberts Spatial calcium buffering in saccular hair cells Nature 363 1993 74 76
    • (1993) Nature , vol.363 , pp. 74-76
    • Roberts, W.M.1
  • 66
    • 0024326915 scopus 로고
    • The calcium-binding site in the galactose chemoreceptor protein. Crystallographic and metal-binding studies
    • M.N. Vyas, B.L. Jacobson, and F.A. Quiocho The calcium-binding site in the galactose chemoreceptor protein. Crystallographic and metal-binding studies J. Biol. Chem. 264 1989 20817 20821
    • (1989) J. Biol. Chem. , vol.264 , pp. 20817-20821
    • Vyas, M.N.1    Jacobson, B.L.2    Quiocho, F.A.3
  • 67
    • 0037228095 scopus 로고    scopus 로고
    • Exchange characteristics of calcium ions bound to anthrax protective antigen
    • S. Gao-Sheridan, S. Zhang, and R.J. Collier Exchange characteristics of calcium ions bound to anthrax protective antigen Biochem. Biophys. Res. Commun. 300 2003 61 64
    • (2003) Biochem. Biophys. Res. Commun. , vol.300 , pp. 61-64
    • Gao-Sheridan, S.1    Zhang, S.2    Collier, R.J.3
  • 68
    • 0024263694 scopus 로고
    • Cell attachment to thrombospondin: The role of ARG-GLY-ASP, calcium, and integrin receptors
    • J. Lawler, R. Weinstein, and R.O. Hynes Cell attachment to thrombospondin: the role of ARG-GLY-ASP, calcium, and integrin receptors J. Cell Biol. 107 1988 2351 2361
    • (1988) J. Cell Biol. , vol.107 , pp. 2351-2361
    • Lawler, J.1    Weinstein, R.2    Hynes, R.O.3


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