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Volumn 371, Issue 3, 2007, Pages 685-702

Crystal Structure of ll-Diaminopimelate Aminotransferase from Arabidopsis thaliana: A Recently Discovered Enzyme in the Biosynthesis of l-Lysine by Plants and Chlamydia

Author keywords

aminotransferase; Arabidopsis thaliana; diaminopimelate; lysine biosynthesis; pyridoxal 5 phosphate

Indexed keywords

AMINOTRANSFERASE; DIAMINOPIMELIC ACID; GLUTAMIC ACID; MALIC ACID; PICOLINIC ACID DERIVATIVE; TETRAHYDRODIPICOLINIC ACID; UNCLASSIFIED DRUG;

EID: 34447618073     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.05.061     Document Type: Article
Times cited : (40)

References (44)
  • 1
    • 33847633444 scopus 로고    scopus 로고
    • Diaminopimelate and lysine biosynthesis- an antimicrobial target in bacteria
    • Vederas J.C. Diaminopimelate and lysine biosynthesis- an antimicrobial target in bacteria. Canad. J. Chem. 84 (2006) 1197-1207
    • (2006) Canad. J. Chem. , vol.84 , pp. 1197-1207
    • Vederas, J.C.1
  • 2
    • 0034076849 scopus 로고    scopus 로고
    • Bacterial diaminopimelate metabolism as a target for antibiotic design
    • Cox R.J., Sutherland A., and Vederas J.C. Bacterial diaminopimelate metabolism as a target for antibiotic design. Bioorg. Med. Chem. 8 (2000) 843-871
    • (2000) Bioorg. Med. Chem. , vol.8 , pp. 843-871
    • Cox, R.J.1    Sutherland, A.2    Vederas, J.C.3
  • 3
    • 0031616883 scopus 로고    scopus 로고
    • Enzymology of bacterial lysine biosynthesis
    • Scapin G., and Blanchard J.S. Enzymology of bacterial lysine biosynthesis. Adv. Enzymol. 72 (1998) 279-324
    • (1998) Adv. Enzymol. , vol.72 , pp. 279-324
    • Scapin, G.1    Blanchard, J.S.2
  • 4
  • 5
    • 0034762821 scopus 로고    scopus 로고
    • Recent advances in the formation of the bacterial peptidoglycan monomer unit
    • van Heijenoort J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nature Prod. Rep. 18 (2001) 503-519
    • (2001) Nature Prod. Rep. , vol.18 , pp. 503-519
    • van Heijenoort, J.1
  • 7
    • 0032931226 scopus 로고    scopus 로고
    • Flux through the tetrahydrodipicolinate succinylase pathway is dispensable for l-Lysine production in Corynebacterium glutamicum
    • Shaw-Reid C.A., McCormick M.M., Sinskey A.J., and Stephanopoulos G. Flux through the tetrahydrodipicolinate succinylase pathway is dispensable for l-Lysine production in Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 51 (1999) 325-333
    • (1999) Appl. Microbiol. Biotechnol. , vol.51 , pp. 325-333
    • Shaw-Reid, C.A.1    McCormick, M.M.2    Sinskey, A.J.3    Stephanopoulos, G.4
  • 8
    • 0033575390 scopus 로고    scopus 로고
    • Gene discovery and product development for grain quality traits
    • Mazur B., Krebbers E., and Tingey S. Gene discovery and product development for grain quality traits. Science 285 (1999) 372-375
    • (1999) Science , vol.285 , pp. 372-375
    • Mazur, B.1    Krebbers, E.2    Tingey, S.3
  • 9
    • 33645808723 scopus 로고    scopus 로고
    • An ll-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants
    • Hudson A.O., Singh B.K., Leustek T., and Gilvarg C. An ll-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiol. 140 (2006) 292-301
    • (2006) Plant Physiol. , vol.140 , pp. 292-301
    • Hudson, A.O.1    Singh, B.K.2    Leustek, T.3    Gilvarg, C.4
  • 10
    • 0034741049 scopus 로고    scopus 로고
    • The first stereospecific synthesis of l-tetrahydrodipicolinic acid; a key intermediate of diaminopimelate metabolism
    • Caplan J.F., Sutherland A., and Vederas J.C. The first stereospecific synthesis of l-tetrahydrodipicolinic acid; a key intermediate of diaminopimelate metabolism. J. Chem. Soc. Perkin Trans. 1 (2001) 2217-2220
    • (2001) J. Chem. Soc. Perkin Trans. , vol.1 , pp. 2217-2220
    • Caplan, J.F.1    Sutherland, A.2    Vederas, J.C.3
  • 11
    • 33845221534 scopus 로고    scopus 로고
    • l,l-Diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine
    • McCoy A.J., Adams N.E., Hudson A.O., Gilvarg C., Leustek T., and Maurelli A.T. l,l-Diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine. Proc. Natl Acad. Sci. USA 103 (2006) 17909-17914
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 17909-17914
    • McCoy, A.J.1    Adams, N.E.2    Hudson, A.O.3    Gilvarg, C.4    Leustek, T.5    Maurelli, A.T.6
  • 12
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 13
    • 33847272515 scopus 로고    scopus 로고
    • The three-dimensional structure of N-succinyldiaminopimelate aminotransferase from Mycobacterium tuberculosis
    • Weyand S., Kefala G., and Weiss M.S. The three-dimensional structure of N-succinyldiaminopimelate aminotransferase from Mycobacterium tuberculosis. J. Mol. Biol. 367 (2007) 825-838
    • (2007) J. Mol. Biol. , vol.367 , pp. 825-838
    • Weyand, S.1    Kefala, G.2    Weiss, M.S.3
  • 14
    • 0031058188 scopus 로고    scopus 로고
    • Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods
    • delaFortelle E., and Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276 (1997) 472-494
    • (1997) Methods Enzymol. , vol.276 , pp. 472-494
    • delaFortelle, E.1    Bricogne, G.2
  • 15
    • 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. Nature Struct. Biol. 6 (1999) 458-463
    • (1999) Nature Struct. Biol. , vol.6 , pp. 458-463
    • Perrakis, A.1    Morris, R.2    Lamzin, V.S.3
  • 16
    • 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
  • 17
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
    • (1994) Acta Crystallog. sect. D , vol.50 , pp. 760-763
  • 19
    • 0343851637 scopus 로고    scopus 로고
    • The manifold of vitamin B6 dependent enzymes
    • Schneider G., Kack H., and Lindqvist Y. The manifold of vitamin B6 dependent enzymes. Structure 8 (2000) R1-R6
    • (2000) Structure , vol.8
    • Schneider, G.1    Kack, H.2    Lindqvist, Y.3
  • 21
    • 3943113663 scopus 로고    scopus 로고
    • Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations
    • Eliot A.C., and Kirsch J.F. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73 (2004) 383-415
    • (2004) Annu. Rev. Biochem. , vol.73 , pp. 383-415
    • Eliot, A.C.1    Kirsch, J.F.2
  • 22
    • 0027297771 scopus 로고
    • Aminotransferases: demonstration of homology and division into evolutionary subgroups
    • Mehta P.K., Hale T.I., and Christen P. Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur. J. Biochem. 214 (1993) 549-561
    • (1993) Eur. J. Biochem. , vol.214 , pp. 549-561
    • Mehta, P.K.1    Hale, T.I.2    Christen, P.3
  • 23
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional protein folds
    • Holm L., and Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucl. Acids Res. 25 (1997) 231-234
    • (1997) Nucl. Acids Res. , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 24
    • 0033596715 scopus 로고    scopus 로고
    • Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate
    • Nakai T., Okada K., Akutsu S., Miyahara I., Kawaguchi S., Kato R., et al. Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. Biochemistry 38 (1999) 2413-2424
    • (1999) Biochemistry , vol.38 , pp. 2413-2424
    • Nakai, T.1    Okada, K.2    Akutsu, S.3    Miyahara, I.4    Kawaguchi, S.5    Kato, R.6
  • 25
    • 33646195686 scopus 로고    scopus 로고
    • Detection of protein assemblies in crystals
    • Berthold M.R., Glen R., Diederichs K., Kohlbacher O., and Fischer I. (Eds), Springer-Verlag, Berlin, Heidelberg
    • Krissinel E., and Henrick K. Detection of protein assemblies in crystals. In: Berthold M.R., Glen R., Diederichs K., Kohlbacher O., and Fischer I. (Eds). Computational Life Sciences, Proceedings vol. 3695 (2005), Springer-Verlag, Berlin, Heidelberg 163-174
    • (2005) Computational Life Sciences, Proceedings , vol.3695 , pp. 163-174
    • Krissinel, E.1    Henrick, K.2
  • 26
    • 0035943396 scopus 로고    scopus 로고
    • Crystal structure of histidinol phosphate aminotransferase (HisC) from Escherichia coli, and its covalent complex with pyridoxal-5′-phosphate and l-histidinol phosphate
    • Sivaraman J., Li Y., Larocque R., Schrag J.D., Cygler M., and Matte A. Crystal structure of histidinol phosphate aminotransferase (HisC) from Escherichia coli, and its covalent complex with pyridoxal-5′-phosphate and l-histidinol phosphate. J. Mol. Biol. 311 (2001) 761-776
    • (2001) J. Mol. Biol. , vol.311 , pp. 761-776
    • Sivaraman, J.1    Li, Y.2    Larocque, R.3    Schrag, J.D.4    Cygler, M.5    Matte, A.6
  • 27
    • 22444440389 scopus 로고    scopus 로고
    • Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage
    • Dubnovitsky A.P., Ravelli R.B., Popov A.N., and Papageorgiou A.C. Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. Protein Sci. 14 (2005) 1498-1507
    • (2005) Protein Sci. , vol.14 , pp. 1498-1507
    • Dubnovitsky, A.P.1    Ravelli, R.B.2    Popov, A.N.3    Papageorgiou, A.C.4
  • 28
    • 0030995422 scopus 로고    scopus 로고
    • Crystal structure of glutamate-1-semialdehyde aminomutase: an alpha2-dimeric vitamin B6-dependent enzyme with asymmetry in structure and active site reactivity
    • Hennig M., Grimm B., Contestabile R., John R.A., and Jansonius J.N. Crystal structure of glutamate-1-semialdehyde aminomutase: an alpha2-dimeric vitamin B6-dependent enzyme with asymmetry in structure and active site reactivity. Proc. Natl Acad. Sci. USA 94 (1997) 4866-4871
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 4866-4871
    • Hennig, M.1    Grimm, B.2    Contestabile, R.3    John, R.A.4    Jansonius, J.N.5
  • 29
    • 33747162722 scopus 로고    scopus 로고
    • The molecular structure of Rv2074, a probable pyridoxine 5′-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 angstroms resolution
    • Biswal B.K., Au K., Cherney M.M., Garen C., and James M.N. The molecular structure of Rv2074, a probable pyridoxine 5′-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 angstroms resolution. Acta Crystallog. sect. F 62 (2006) 735-742
    • (2006) Acta Crystallog. sect. F , vol.62 , pp. 735-742
    • Biswal, B.K.1    Au, K.2    Cherney, M.M.3    Garen, C.4    James, M.N.5
  • 31
    • 0037646540 scopus 로고    scopus 로고
    • Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
    • Hayashi H., Mizuguchi H., Miyahara I., Nakajima Y., Hirotsu K., and Kagamiyama H. Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis. J. Biol. Chem. 278 (2003) 9481-9488
    • (2003) J. Biol. Chem. , vol.278 , pp. 9481-9488
    • Hayashi, H.1    Mizuguchi, H.2    Miyahara, I.3    Nakajima, Y.4    Hirotsu, K.5    Kagamiyama, H.6
  • 32
    • 0034098693 scopus 로고    scopus 로고
    • The role of residues outside the active site: structural basis for function of C191 mutants of Escherichia coli aspartate aminotransferase
    • Jeffery C.J., Gloss L.M., Petsko G.A., and Ringe D. The role of residues outside the active site: structural basis for function of C191 mutants of Escherichia coli aspartate aminotransferase. Protein Eng. 13 (2000) 105-112
    • (2000) Protein Eng. , vol.13 , pp. 105-112
    • Jeffery, C.J.1    Gloss, L.M.2    Petsko, G.A.3    Ringe, D.4
  • 33
    • 0028876895 scopus 로고
    • Substitution of apolar residues in the active site of aspartate aminotransferase by histidine. Effects on reaction and substrate specificity
    • Vacca R.A., Christen P., Malashkevich V.N., Jansonius J.N., and Sandmeier E. Substitution of apolar residues in the active site of aspartate aminotransferase by histidine. Effects on reaction and substrate specificity. Eur. J. Biochem. 227 (1995) 481-487
    • (1995) Eur. J. Biochem. , vol.227 , pp. 481-487
    • Vacca, R.A.1    Christen, P.2    Malashkevich, V.N.3    Jansonius, J.N.4    Sandmeier, E.5
  • 34
    • 0028174289 scopus 로고
    • Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms
    • Jager J., Moser M., Sauder U., and Jansonius J.N. Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms. J. Mol. Biol. 239 (1994) 285-305
    • (1994) J. Mol. Biol. , vol.239 , pp. 285-305
    • Jager, J.1    Moser, M.2    Sauder, U.3    Jansonius, J.N.4
  • 35
    • 0028167665 scopus 로고
    • X-ray crystallographic study of pyridoxal 5′-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form
    • Okamoto A., Higuchi T., Hirotsu K., Kuramitsu S., and Kagamiyama H. X-ray crystallographic study of pyridoxal 5′-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form. J. Biochem. (Tokyo) 116 (1994) 95-107
    • (1994) J. Biochem. (Tokyo) , vol.116 , pp. 95-107
    • Okamoto, A.1    Higuchi, T.2    Hirotsu, K.3    Kuramitsu, S.4    Kagamiyama, H.5
  • 36
    • 0032555280 scopus 로고    scopus 로고
    • The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase
    • Beaman T.W., Blanchard J.S., and Roderick S.L. The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase. Biochemistry 37 (1998) 10363-10369
    • (1998) Biochemistry , vol.37 , pp. 10363-10369
    • Beaman, T.W.1    Blanchard, J.S.2    Roderick, S.L.3
  • 37
    • 0031045585 scopus 로고    scopus 로고
    • Preparation of selenomethionyl proteins for phase determination
    • Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276 (1997) 523-530
    • (1997) Methods Enzymol. , vol.276 , pp. 523-530
    • Doublie, S.1
  • 38
    • 0027439390 scopus 로고
    • Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
    • Van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L., and Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229 (1993) 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
  • 39
    • 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
  • 40
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: an automated program for molecular replacement
    • Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallog. 30 (1997) 1022-1025
    • (1997) J. Appl. Crystallog. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 41
  • 42
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., and Sander C. 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
  • 43
    • 0043123208 scopus 로고    scopus 로고
    • ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins
    • Gouet P., Robert X., and Courcelle E. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucl. Acids Res. 31 (2003) 3320-3323
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3320-3323
    • Gouet, P.1    Robert, X.2    Courcelle, E.3
  • 44
    • 0001679473 scopus 로고    scopus 로고
    • ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions
    • Cohen G.H. ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions. J. Appl. Crystallog. 30 (1997) 1160-1161
    • (1997) J. Appl. Crystallog. , vol.30 , pp. 1160-1161
    • Cohen, G.H.1


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