메뉴 건너뛰기




Volumn 382, Issue 1, 2008, Pages 99-111

Crystal Structure of a Glutamate/Aspartate Binding Protein Complexed with a Glutamate Molecule: Structural Basis of Ligand Specificity at Atomic Resolution

Author keywords

crystal structure; ligand binding; periplasmic binding protein; structural basis of specificity; ultrahigh resolution

Indexed keywords

ASPARTATE GLUTAMATE BINDING PROTEIN; ASPARTIC ACID; BINDING PROTEIN; GLUTAMIC ACID; LIGAND; SERINE;

EID: 49349094496     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.06.091     Document Type: Article
Times cited : (25)

References (37)
  • 1
    • 0022555851 scopus 로고
    • Bacterial periplasmic transport systems: structure, mechanism, and evolution
    • Ames G.F. Bacterial periplasmic transport systems: structure, mechanism, and evolution. Annu. Rev. Biochem. 55 (1986) 397-425
    • (1986) Annu. Rev. Biochem. , vol.55 , pp. 397-425
    • Ames, G.F.1
  • 2
    • 33947154878 scopus 로고    scopus 로고
    • Structure of an ABC transporter in complex with its binding protein
    • Hollenstein K., Frei D.C., and Locher K.P. Structure of an ABC transporter in complex with its binding protein. Nature 446 (2007) 213-216
    • (2007) Nature , vol.446 , pp. 213-216
    • Hollenstein, K.1    Frei, D.C.2    Locher, K.P.3
  • 3
    • 36549018568 scopus 로고    scopus 로고
    • Crystal structure of a catalytic intermediate of the maltose transporter
    • Oldham M.L., Khare D., Quiocho F.A., Davidson A.L., and Chen J. Crystal structure of a catalytic intermediate of the maltose transporter. Nature 450 (2007) 515-521
    • (2007) Nature , vol.450 , pp. 515-521
    • Oldham, M.L.1    Khare, D.2    Quiocho, F.A.3    Davidson, A.L.4    Chen, J.5
  • 4
    • 0024563996 scopus 로고
    • Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine
    • Sack J.S., Saper M.A., and Quiocho F.A. Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine. J. Mol. Biol. 206 (1989) 171-191
    • (1989) J. Mol. Biol. , vol.206 , pp. 171-191
    • Sack, J.S.1    Saper, M.A.2    Quiocho, F.A.3
  • 5
    • 0024511371 scopus 로고
    • Structure of the l-leucine-binding protein refined at 2.4 Å resolution and comparison with the Leu/Ile/Val-binding protein structure
    • Sack J.S., Trakhanov S.D., Tsigannik I.H., and Quiocho F.A. Structure of the l-leucine-binding protein refined at 2.4 Å resolution and comparison with the Leu/Ile/Val-binding protein structure. J. Mol. Biol. 206 (1989) 193-207
    • (1989) J. Mol. Biol. , vol.206 , pp. 193-207
    • Sack, J.S.1    Trakhanov, S.D.2    Tsigannik, I.H.3    Quiocho, F.A.4
  • 6
    • 0026321096 scopus 로고
    • Crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium at 2.7 Å resolution
    • Kang C.H., Shin W.C., Yamagata Y., Gokcen S., Ames G.F., and Kim S.H. Crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium at 2.7 Å resolution. J. Biol. Chem. 266 (1991) 23893-23899
    • (1991) J. Biol. Chem. , vol.266 , pp. 23893-23899
    • Kang, C.H.1    Shin, W.C.2    Yamagata, Y.3    Gokcen, S.4    Ames, G.F.5    Kim, S.H.6
  • 7
    • 0028067178 scopus 로고
    • The bacterial periplasmic histidine-binding protein: structure/function analysis of the ligand-binding site and comparison with related proteins
    • Oh B.H., Kang C.H., De Bondt H., Kim S.H., Nikaido K., Joshi A.K., and Ames G.F. The bacterial periplasmic histidine-binding protein: structure/function analysis of the ligand-binding site and comparison with related proteins. J. Biol. Chem. 269 (1994) 4135-4143
    • (1994) J. Biol. Chem. , vol.269 , pp. 4135-4143
    • Oh, B.H.1    Kang, C.H.2    De Bondt, H.3    Kim, S.H.4    Nikaido, K.5    Joshi, A.K.6    Ames, G.F.7
  • 8
    • 0028174670 scopus 로고
    • Refined 1.89-Å structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins
    • Yao N., Trakhanov S., and Quiocho F.A. Refined 1.89-Å structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins. Biochemistry 33 (1994) 4769-4779
    • (1994) Biochemistry , vol.33 , pp. 4769-4779
    • Yao, N.1    Trakhanov, S.2    Quiocho, F.A.3
  • 9
    • 0032562651 scopus 로고    scopus 로고
    • The structure of glutamine-binding protein complexed with glutamine at 1.94 Å resolution: comparisons with other amino acid binding proteins
    • Sun Y.J., Rose J., Wang B.C., and Hsiao C.D. The structure of glutamine-binding protein complexed with glutamine at 1.94 Å resolution: comparisons with other amino acid binding proteins. J. Mol. Biol. 278 (1998) 219-229
    • (1998) J. Mol. Biol. , vol.278 , pp. 219-229
    • Sun, Y.J.1    Rose, J.2    Wang, B.C.3    Hsiao, C.D.4
  • 11
    • 11244349700 scopus 로고    scopus 로고
    • Structural evidence that the 32-kilodalton lipoprotein (Tp32) of Treponema pallidum is an l-methionine-binding protein
    • Deka R.K., Neil L., Hagman K.E., Machius M., Tomchick D.R., Brautigam C.A., and Norgard M.V. Structural evidence that the 32-kilodalton lipoprotein (Tp32) of Treponema pallidum is an l-methionine-binding protein. J. Biol. Chem. 279 (2004) 55644-55650
    • (2004) J. Biol. Chem. , vol.279 , pp. 55644-55650
    • Deka, R.K.1    Neil, L.2    Hagman, K.E.3    Machius, M.4    Tomchick, D.R.5    Brautigam, C.A.6    Norgard, M.V.7
  • 12
    • 21244445047 scopus 로고    scopus 로고
    • An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein
    • Müller A., Thomas G.H., Horler R., Brannigan J.A., Blagova E., Levdikov V.M., et al. An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein. Mol. Microbiol. 57 (2005) 143-155
    • (2005) Mol. Microbiol. , vol.57 , pp. 143-155
    • Müller, A.1    Thomas, G.H.2    Horler, R.3    Brannigan, J.A.4    Blagova, E.5    Levdikov, V.M.6
  • 13
    • 34547654290 scopus 로고    scopus 로고
    • A bacterial virulence factor with a dual role as an adhesin and a solute-binding protein: the crystal structure at 1.5 Å resolution of the PEB1a protein from the food-borne human pathogen Campylobacter jejuni
    • Müller A., Leon-Kempis M.D.R., Dodson E., Wilson K.S., Wilkinson A.J., and Kelly D.J. A bacterial virulence factor with a dual role as an adhesin and a solute-binding protein: the crystal structure at 1.5 Å resolution of the PEB1a protein from the food-borne human pathogen Campylobacter jejuni. J. Mol. Biol. 372 (2007) 160-171
    • (2007) J. Mol. Biol. , vol.372 , pp. 160-171
    • Müller, A.1    Leon-Kempis, M.D.R.2    Dodson, E.3    Wilson, K.S.4    Wilkinson, A.J.5    Kelly, D.J.6
  • 14
    • 0016745498 scopus 로고
    • Purification and properties of a periplasmic glutamate-aspartate binding protein from Escherichia coli K12 strain W3092
    • Willis R.C., and Furlong C.E. Purification and properties of a periplasmic glutamate-aspartate binding protein from Escherichia coli K12 strain W3092. J. Biol. Chem. 250 (1975) 2574-2580
    • (1975) J. Biol. Chem. , vol.250 , pp. 2574-2580
    • Willis, R.C.1    Furlong, C.E.2
  • 15
    • 0016709741 scopus 로고
    • Interactions of a glutamate-aspartate binding protein with the glutamate transport system of Escherichia coli
    • Willis R.C., and Furlong C.E. Interactions of a glutamate-aspartate binding protein with the glutamate transport system of Escherichia coli. J. Biol. Chem. 250 (1975) 2581-2586
    • (1975) J. Biol. Chem. , vol.250 , pp. 2581-2586
    • Willis, R.C.1    Furlong, C.E.2
  • 16
    • 33646415394 scopus 로고    scopus 로고
    • A periplasmic glutamate/aspartate binding protein from Shigella flexneri: gene cloning, over-expression, purification and preliminary crystallographic studies of the recombinant protein
    • Fan C.P., Zhu D.Y., Lu H.X., Jin Q., and Wang D.C. A periplasmic glutamate/aspartate binding protein from Shigella flexneri: gene cloning, over-expression, purification and preliminary crystallographic studies of the recombinant protein. Protein Pept. Lett. 13 (2006) 513-516
    • (2006) Protein Pept. Lett. , vol.13 , pp. 513-516
    • Fan, C.P.1    Zhu, D.Y.2    Lu, H.X.3    Jin, Q.4    Wang, D.C.5
  • 17
    • 4143115810 scopus 로고    scopus 로고
    • Periplasmic binding proteins: a versatile superfamily for protein engineering
    • Dwyer M.A., and Hellinga H.W. Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr. Opin. Struct. Biol. 14 (2004) 495-504
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 495-504
    • Dwyer, M.A.1    Hellinga, H.W.2
  • 18
  • 19
    • 0000319698 scopus 로고
    • Atomic structures and function of periplasmic receptors for active transport and chemotaxis
    • Quiocho F.A. Atomic structures and function of periplasmic receptors for active transport and chemotaxis. Curr. Opin. Struct. Biol. 1 (1991) 922-933
    • (1991) Curr. Opin. Struct. Biol. , vol.1 , pp. 922-933
    • Quiocho, F.A.1
  • 20
    • 0025716317 scopus 로고
    • Atomic structures of periplasmic binding proteins and the high-affinity active transport systems in bacteria
    • Quiocho F.A. Atomic structures of periplasmic binding proteins and the high-affinity active transport systems in bacteria. Philos. Trans. R. Soc. London, Ser. B 326 (1990) 341-351
    • (1990) Philos. Trans. R. Soc. London, Ser. B , vol.326 , pp. 341-351
    • Quiocho, F.A.1
  • 21
    • 34047266662 scopus 로고    scopus 로고
    • The structure of a cyanobacterial bicarbonate transport protein, CmpA
    • Koropatkin N.M., Koppenaal D.W., Pakrasi H.B., and Smith T.J. The structure of a cyanobacterial bicarbonate transport protein, CmpA. J. Biol. Chem. 282 (2007) 2606-2614
    • (2007) J. Biol. Chem. , vol.282 , pp. 2606-2614
    • Koropatkin, N.M.1    Koppenaal, D.W.2    Pakrasi, H.B.3    Smith, T.J.4
  • 22
    • 0033548125 scopus 로고    scopus 로고
    • Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history
    • Fukami-Kobayashi K., Tateno Y., and Nishikawa K. Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. J. Mol. Biol. 286 (1999) 279-290
    • (1999) J. Mol. Biol. , vol.286 , pp. 279-290
    • Fukami-Kobayashi, K.1    Tateno, Y.2    Nishikawa, K.3
  • 23
    • 0027235488 scopus 로고
    • Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand
    • Oh B.H., Pandit J., Kang C.H., Nikaido K., Gokcen S., Ames G.F., and Kim S.H. Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand. J. Biol. Chem. 268 (1993) 11348-11355
    • (1993) J. Biol. Chem. , vol.268 , pp. 11348-11355
    • Oh, B.H.1    Pandit, J.2    Kang, C.H.3    Nikaido, K.4    Gokcen, S.5    Ames, G.F.6    Kim, S.H.7
  • 24
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt G.J., and Jones T.A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 (1994) 178-185
    • (1994) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 25
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word J.M., Lovell S.C., Richardson J.S., and Richardson D.C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285 (1999) 1735-1747
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 26
    • 0034866668 scopus 로고    scopus 로고
    • Decomposition of protein tryptophan fluorescence spectra into log-normal components. I. Decomposition algorithms
    • Burstein E.A., Abornev S.M., and Reshetnyak Y.K. Decomposition of protein tryptophan fluorescence spectra into log-normal components. I. Decomposition algorithms. Biophys. J. 81 (2001) 1699-1709
    • (2001) Biophys. J. , vol.81 , pp. 1699-1709
    • Burstein, E.A.1    Abornev, S.M.2    Reshetnyak, Y.K.3
  • 27
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 31
    • 0032964481 scopus 로고    scopus 로고
    • Automated protein model building combined with iterative structure refinement
    • Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6 (1999) 458-463
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 458-463
    • Perrakis, A.1    Morris, R.2    Lamzin, V.S.3
  • 32
    • 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 M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., Sect. A: Found. Crystallogr. 47 (1991) 110-119
    • (1991) Acta Crystallogr., Sect. A: Found. Crystallogr. , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 33
  • 34
    • 0027412196 scopus 로고
    • ALSCRIPT: a tool to format multiple sequence alignments
    • Barton G.J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6 (1993) 37-40
    • (1993) Protein Eng. , vol.6 , pp. 37-40
    • Barton, G.J.1
  • 35
    • 0026244229 scopus 로고
    • MOLSCRIPT-a program to produce both detailed and schematic plots of protein structures
    • Kraulis P.J. MOLSCRIPT-a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24 (1991) 946-950
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 36
    • 0033119938 scopus 로고    scopus 로고
    • Further additions to MolScript version 1.4, including reading and contouring of electron-density maps
    • Esnouf R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (1999) 938-940
    • (1999) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.55 , pp. 938-940
    • Esnouf, R.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.