메뉴 건너뛰기




Volumn 393, Issue 2, 2009, Pages 425-434

Crystal Structure of the Hexameric Catabolic Ornithine Transcarbamylase from Lactobacillus hilgardii: Structural Insights into the Oligomeric Assembly and Metal Binding

Author keywords

crystal structure; metal binding; oligomeric assembly; ornithine transcarbamylase

Indexed keywords

ARGININE; ARGININE DEIMINASE; CARBAMOYL PHOSPHATE; CITRULLINE; OLIGOMER; ORNITHINE; ORNITHINE CARBAMOYLTRANSFERASE; BACTERIAL PROTEIN; NICKEL;

EID: 70349420814     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.08.002     Document Type: Article
Times cited : (16)

References (40)
  • 1
    • 0017623937 scopus 로고
    • Anabolic ornithine carbamoyltransferase of Pseudomonas. The bases of its functional specialization
    • Stalon V., Legrain C., and Wiame J.M. Anabolic ornithine carbamoyltransferase of Pseudomonas. The bases of its functional specialization. Eur. J. Biochem. 74 (1977) 319-327
    • (1977) Eur. J. Biochem. , vol.74 , pp. 319-327
    • Stalon, V.1    Legrain, C.2    Wiame, J.M.3
  • 2
    • 0018673918 scopus 로고
    • Genetic and physiological characterization of Pseudomonas aeruginosa mutants affected in the catabolic ornithine carbamoyltransferase
    • Haas D., Evans R., Mercenier A., Simon J.P., and Stalon V. Genetic and physiological characterization of Pseudomonas aeruginosa mutants affected in the catabolic ornithine carbamoyltransferase. J. Bacteriol. 139 (1979) 713-720
    • (1979) J. Bacteriol. , vol.139 , pp. 713-720
    • Haas, D.1    Evans, R.2    Mercenier, A.3    Simon, J.P.4    Stalon, V.5
  • 3
    • 0024998366 scopus 로고
    • Converting catabolic ornithine carbamoyltransferase to an anabolic enzyme
    • Baur H., Tricot C., Stalon V., and Haas D. Converting catabolic ornithine carbamoyltransferase to an anabolic enzyme. J. Biol. Chem. 265 (1990) 14728-14731
    • (1990) J. Biol. Chem. , vol.265 , pp. 14728-14731
    • Baur, H.1    Tricot, C.2    Stalon, V.3    Haas, D.4
  • 4
    • 70349431606 scopus 로고
    • Steady-state kinetics and analysis of pH dependence on wild-type and a modified allosteric Pseudomonas aeruginosa ornithine carbamoyltransferase containing the replacement of glutamate 105 by alanine
    • Tricot C., Nguyen V.T., and Stalon V. Steady-state kinetics and analysis of pH dependence on wild-type and a modified allosteric Pseudomonas aeruginosa ornithine carbamoyltransferase containing the replacement of glutamate 105 by alanine. Eur. J. Biochem. 221 (1993) 555-561
    • (1993) Eur. J. Biochem. , vol.221 , pp. 555-561
    • Tricot, C.1    Nguyen, V.T.2    Stalon, V.3
  • 5
    • 0032582483 scopus 로고    scopus 로고
    • Allosteric regulation in Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase revisited: association of concerted homotropic cooperative interactions and local heterotropic effects
    • Tricot C., Villeret V., Sainz G., Dideberg O., and Stalon V. Allosteric regulation in Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase revisited: association of concerted homotropic cooperative interactions and local heterotropic effects. J. Mol. Biol. 283 (1998) 695-704
    • (1998) J. Mol. Biol. , vol.283 , pp. 695-704
    • Tricot, C.1    Villeret, V.2    Sainz, G.3    Dideberg, O.4    Stalon, V.5
  • 6
    • 0032518449 scopus 로고    scopus 로고
    • Kinetic studies of allosteric catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa
    • Sainz G., Tricot C., Foray M.F., Marion D., Dideberg O., and Stalon V. Kinetic studies of allosteric catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Eur. J. Biochem. 251 (1998) 528-533
    • (1998) Eur. J. Biochem. , vol.251 , pp. 528-533
    • Sainz, G.1    Tricot, C.2    Foray, M.F.3    Marion, D.4    Dideberg, O.5    Stalon, V.6
  • 7
    • 0028881913 scopus 로고
    • Crystal structure of Pseudomonas aeruginosa catabolic ornithine transcarbamoylase at 3.0-Å resolution: a different oligomeric organization in the transcarbamoylase family
    • Villeret V., Tricot C., Stalon V., and Dideberg O. Crystal structure of Pseudomonas aeruginosa catabolic ornithine transcarbamoylase at 3.0-Å resolution: a different oligomeric organization in the transcarbamoylase family. Proc. Natl Acad. Sci. USA 92 (1995) 10762-10766
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 10762-10766
    • Villeret, V.1    Tricot, C.2    Stalon, V.3    Dideberg, O.4
  • 8
    • 0023369209 scopus 로고
    • Primary and quaternary structure of the catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Extensive sequence homology with the anabolic ornithine carbamoyltransferases of Escherichia coli
    • Baur H., Stalon V., Falmagne P., Lüthi E., and Haas D. Primary and quaternary structure of the catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Extensive sequence homology with the anabolic ornithine carbamoyltransferases of Escherichia coli. Eur. J. Biochem. 166 (1987) 111-117
    • (1987) Eur. J. Biochem. , vol.166 , pp. 111-117
    • Baur, H.1    Stalon, V.2    Falmagne, P.3    Lüthi, E.4    Haas, D.5
  • 9
    • 0025881316 scopus 로고
    • Molecular size and symmetry of Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase. An X-ray crystallography analysis
    • Marcq S., Díaz-Ruano A., Charlier P., Dideberg O., Tricot C., Piérard A., and Stalon V. Molecular size and symmetry of Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase. An X-ray crystallography analysis. J. Mol. Biol. 220 (1991) 9-12
    • (1991) J. Mol. Biol. , vol.220 , pp. 9-12
    • Marcq, S.1    Díaz-Ruano, A.2    Charlier, P.3    Dideberg, O.4    Tricot, C.5    Piérard, A.6    Stalon, V.7
  • 10
    • 0029864712 scopus 로고    scopus 로고
    • Catabolic ornithine carbamoyltransferase of Pseudomonas aeruginosa. Importance of the N-terminal region for dodecameric structure and homotropic carbamoylphosphate cooperativity
    • Nguyen V.T., Baker D.P., Tricot C., Baur H., Villeret V., Dideberg O., et al. Catabolic ornithine carbamoyltransferase of Pseudomonas aeruginosa. Importance of the N-terminal region for dodecameric structure and homotropic carbamoylphosphate cooperativity. Eur. J. Biochem. 236 (1996) 283-293
    • (1996) Eur. J. Biochem. , vol.236 , pp. 283-293
    • Nguyen, V.T.1    Baker, D.P.2    Tricot, C.3    Baur, H.4    Villeret, V.5    Dideberg, O.6
  • 11
    • 0028144138 scopus 로고
    • Aspartate transcarbamylase from Escherichia coli: activity and regulation
    • Lipscomb W.N. Aspartate transcarbamylase from Escherichia coli: activity and regulation. Adv. Enzymol. Relat. Areas Mol. Biol 68 (1994) 67-152
    • (1994) Adv. Enzymol. Relat. Areas Mol. Biol , vol.68 , pp. 67-152
    • Lipscomb, W.N.1
  • 12
    • 0032545106 scopus 로고    scopus 로고
    • 1.85-Å resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-l-ornithine. Catalytic mechanism and correlation with inherited deficiency
    • Shi D., Morizono H., Ha Y., Aoyagi M., Tuchman M., and Allewell N. 1.85-Å resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-l-ornithine. Catalytic mechanism and correlation with inherited deficiency. J. Biol. Chem. 273 (1998) 34247-34254
    • (1998) J. Biol. Chem. , vol.273 , pp. 34247-34254
    • Shi, D.1    Morizono, H.2    Ha, Y.3    Aoyagi, M.4    Tuchman, M.5    Allewell, N.6
  • 13
    • 0034212938 scopus 로고    scopus 로고
    • Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and l-norvaline at 1.9 Å resolution
    • Shi D., Morizono H., Aoyagi M., Tuchman M., and Allewell N. Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and l-norvaline at 1.9 Å resolution. Proteins: Struct. Funct. Genet. 39 (2000) 271-277
    • (2000) Proteins: Struct. Funct. Genet. , vol.39 , pp. 271-277
    • Shi, D.1    Morizono, H.2    Aoyagi, M.3    Tuchman, M.4    Allewell, N.5
  • 14
    • 0030802657 scopus 로고    scopus 로고
    • Crystal structure at 2.8 Å resolution of anabolic ornithine transcarbamylase from Escherichia coli
    • Jin L., Seaton B.A., and Head J.F. Crystal structure at 2.8 Å resolution of anabolic ornithine transcarbamylase from Escherichia coli. Nat. Struct. Biol. 4 (1997) 622-625
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 622-625
    • Jin, L.1    Seaton, B.A.2    Head, J.F.3
  • 15
    • 0030967422 scopus 로고    scopus 로고
    • Substrate-induced conformational change in a trimeric ornithine transcarbamoylase
    • Ha Y., McCann M.T., Tuchman M., and Allewell N. Substrate-induced conformational change in a trimeric ornithine transcarbamoylase. Proc. Natl Acad. Sci. USA 94 (1997) 9550-9555
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 9550-9555
    • Ha, Y.1    McCann, M.T.2    Tuchman, M.3    Allewell, N.4
  • 16
    • 0034733518 scopus 로고    scopus 로고
    • δ-(N′-sulfodiaminophosphinyl)-l-ornithine, a true transition state analogue? Crystal structure and implications for catalytic mechanism
    • δ-(N′-sulfodiaminophosphinyl)-l-ornithine, a true transition state analogue? Crystal structure and implications for catalytic mechanism. J. Biol. Chem. 275 (2000) 20012-20019
    • (2000) J. Biol. Chem. , vol.275 , pp. 20012-20019
    • Langley, D.B.1    Templeton, M.2    Fields, B.A.3    Mitchell, R.E.4    Collyer, C.A.5
  • 17
    • 0032539795 scopus 로고    scopus 로고
    • The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures
    • Villeret V., Clantin B., Tricot C., Legrain C., Roovers M., Stalon V., et al. The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures. Proc. Natl Acad. Sci. USA 95 (1998) 2801-2806
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 2801-2806
    • Villeret, V.1    Clantin, B.2    Tricot, C.3    Legrain, C.4    Roovers, M.5    Stalon, V.6
  • 18
    • 37449003424 scopus 로고    scopus 로고
    • The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and l-norvaline reveal the enzyme's catalytic mechanism
    • Sankaranarayanan R., Cherney M.M., Cherney L.T., Garen C.R., Moradian F., and James M.N.G. The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and l-norvaline reveal the enzyme's catalytic mechanism. J. Mol. Biol. 375 (2008) 1052-1063
    • (2008) J. Mol. Biol. , vol.375 , pp. 1052-1063
    • Sankaranarayanan, R.1    Cherney, M.M.2    Cherney, L.T.3    Garen, C.R.4    Moradian, F.5    James, M.N.G.6
  • 20
    • 34548232365 scopus 로고    scopus 로고
    • Inference of 5macromolecular assemblies from crystalline state
    • Krissinel E., and Henrick K. Inference of 5macromolecular assemblies from crystalline state. J. Mol. Biol. 372 (2007) 774-797
    • (2007) J. Mol. Biol. , vol.372 , pp. 774-797
    • Krissinel, E.1    Henrick, K.2
  • 21
    • 0022419375 scopus 로고
    • Aromatic-aromatic interaction. A mechanism of protein-structure stabilization
    • Burley S.K., and Petsko G.A. Aromatic-aromatic interaction. A mechanism of protein-structure stabilization. Science 229 (1985) 23-28
    • (1985) Science , vol.229 , pp. 23-28
    • Burley, S.K.1    Petsko, G.A.2
  • 24
    • 0023836342 scopus 로고
    • A cadmium-binding protein in rat-liver identified as ornithine carbamoyltransferase
    • Aoki Y., Sunaga H., and Suzuki K.T. A cadmium-binding protein in rat-liver identified as ornithine carbamoyltransferase. Biochem. J. 250 (1988) 735-742
    • (1988) Biochem. J. , vol.250 , pp. 735-742
    • Aoki, Y.1    Sunaga, H.2    Suzuki, K.T.3
  • 25
    • 0025192589 scopus 로고
    • 2+ regulation of ornithine transcarbamylase. II. Metal-binding site
    • 2+ regulation of ornithine transcarbamylase. II. Metal-binding site. J. Mol. Biol. 211 (1990) 271-280
    • (1990) J. Mol. Biol. , vol.211 , pp. 271-280
    • Kuo, L.C.1    Caron, C.2    Lee, S.3    Herzberg, W.4
  • 26
    • 0035868405 scopus 로고    scopus 로고
    • Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
    • Shi D., Morizono H., Yu X., Tong L., Allewell N.M., and Tuchman M. Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes. Biochem. J. 354 (2001) 501-509
    • (2001) Biochem. J. , vol.354 , pp. 501-509
    • Shi, D.1    Morizono, H.2    Yu, X.3    Tong, L.4    Allewell, N.M.5    Tuchman, M.6
  • 27
    • 34447331659 scopus 로고    scopus 로고
    • Overexpression, purification, crystallization and preliminary structural studies of catabolic ornithine transcarbamylase from Lactobacillus hilgardii
    • de las Rivas B., Rodríguez H., Angulo I., Muñoz R., and Mancheño J.M. Overexpression, purification, crystallization and preliminary structural studies of catabolic ornithine transcarbamylase from Lactobacillus hilgardii. Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 63 (2007) 563-567
    • (2007) Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. , vol.63 , pp. 563-567
    • de las Rivas, B.1    Rodríguez, H.2    Angulo, I.3    Muñoz, R.4    Mancheño, J.M.5
  • 28
    • 34250329984 scopus 로고    scopus 로고
    • Expression vectors for enzyme restriction- and ligation-independent cloning for producing recombinant His-fusion proteins
    • de las Rivas B., Curiel J.A., Mancheño J.M., and Muñoz R. Expression vectors for enzyme restriction- and ligation-independent cloning for producing recombinant His-fusion proteins. Biotechnol. Prog. 23 (2007) 680-686
    • (2007) Biotechnol. Prog. , vol.23 , pp. 680-686
    • de las Rivas, B.1    Curiel, J.A.2    Mancheño, J.M.3    Muñoz, R.4
  • 29
    • 0037073419 scopus 로고    scopus 로고
    • The arginine deiminase pathway in the wine lactic acid bacterium Lactobacillus hilgardii X1B: structural and functional study of the arcABC genes
    • Arena M.E., Manca de Nadra M.C., and Muñoz R. The arginine deiminase pathway in the wine lactic acid bacterium Lactobacillus hilgardii X1B: structural and functional study of the arcABC genes. Gene 301 (2002) 61-66
    • (2002) Gene , vol.301 , pp. 61-66
    • Arena, M.E.1    Manca de Nadra, M.C.2    Muñoz, R.3
  • 32
    • 33847221102 scopus 로고    scopus 로고
    • A multiplatform code for the analysis of energy-dispersive X-ray fluorescence spectra
    • Solé V.A., Papillon E., Cotte M., Walter Ph., and Susini J. A multiplatform code for the analysis of energy-dispersive X-ray fluorescence spectra. Spectrochim. Acta B 62 (2007) 63-68
    • (2007) Spectrochim. Acta B , vol.62 , pp. 63-68
    • Solé, V.A.1    Papillon, E.2    Cotte, M.3    Walter, Ph.4    Susini, J.5
  • 33
    • 0003076963 scopus 로고
    • Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newslett
    • Leslie A.G.W. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newslett. Protein Crystallogr. 26 (1992)
    • (1992) Protein Crystallogr. , vol.26
    • Leslie, A.G.W.1
  • 34
    • 0028103275 scopus 로고
    • Collaborative Computational Project, Number 4
    • Collaborative Computational Project, Number 4. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 (1994) 760-763
    • (1994) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.50 , pp. 760-763
  • 35
    • 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. Crystallogr. 30 (1997) 1022-1025
    • (1997) J. Appl. Crystallogr. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 37
    • 0032964481 scopus 로고    scopus 로고
    • Automated protein model building combined with iterative structure refinement
    • Perrakis A., Morris R., and Lamzib 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    Lamzib, V.S.3
  • 38
    • 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., Cowtan S.W., and Kjelgaard M. 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    Cowtan, S.W.3    Kjelgaard, M.4
  • 39
    • 0000243829 scopus 로고
    • PROCHECK-a program to check the stereochemical quality of protein structures
    • Laskowski R., MacArthur M., Moss D., and Thornton J.M. PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.1    MacArthur, M.2    Moss, D.3    Thornton, J.M.4
  • 40
    • 84893482610 scopus 로고
    • Solution for best rotation to relate 2 sets of vectors
    • Kabsch W. Solution for best rotation to relate 2 sets of vectors. Acta Crystallogr., Sect. A. 32 (1976) 922-923
    • (1976) Acta Crystallogr., Sect. A. , vol.32 , pp. 922-923
    • Kabsch, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.