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Volumn 386, Issue 2, 2009, Pages 486-503

Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member

Author keywords

2,3 dimethylmalate lyase; citramalate lyase; function annotation; nicotinate pathway; PEP mutase isocitrate lyase superfamily

Indexed keywords

2,3 DIMETHYLMALATE LYASE; 3,3 DIFLUOROOXALOACETATE; HYDROLASE; ISOCITRATE LYASE; NICOTINAMIDE; NICOTINIC ACID; OXALOACETATE ACETYLHYDROLASE; OXALOACETIC ACID DERIVATIVE; UNCLASSIFIED DRUG;

EID: 59149094101     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.12.037     Document Type: Article
Times cited : (13)

References (42)
  • 1
    • 0034656088 scopus 로고    scopus 로고
    • The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans
    • Britton K., Langridge S., Baker P.J., Weeradechapon K., Sedelnikova S.E., De Lucas J.R., et al. The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans. Structure 8 (2000) 349-362
    • (2000) Structure , vol.8 , pp. 349-362
    • Britton, K.1    Langridge, S.2    Baker, P.J.3    Weeradechapon, K.4    Sedelnikova, S.E.5    De Lucas, J.R.6
  • 2
    • 0033135180 scopus 로고    scopus 로고
    • Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate
    • Huang K., Li Z., Jia Y., Dunaway-Mariano D., and Herzberg O. Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate. Structure 7 (1999) 539-548
    • (1999) Structure , vol.7 , pp. 539-548
    • Huang, K.1    Li, Z.2    Jia, Y.3    Dunaway-Mariano, D.4    Herzberg, O.5
  • 3
    • 14344264331 scopus 로고    scopus 로고
    • Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution
    • Liu S., Lu Z., Han Y., Melamud E., Dunaway-Mariano D., and Herzberg O. Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution. Biochemistry 44 (2005) 2949-2962
    • (2005) Biochemistry , vol.44 , pp. 2949-2962
    • Liu, S.1    Lu, Z.2    Han, Y.3    Melamud, E.4    Dunaway-Mariano, D.5    Herzberg, O.6
  • 5
    • 33749010624 scopus 로고    scopus 로고
    • Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily
    • Chen C.C., Han Y., Niu W., Kulakova A.N., Howard A., Quinn J.P., et al. Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily. Biochemistry 45 (2006) 11491-11504
    • (2006) Biochemistry , vol.45 , pp. 11491-11504
    • Chen, C.C.1    Han, Y.2    Niu, W.3    Kulakova, A.N.4    Howard, A.5    Quinn, J.P.6
  • 6
    • 37849018387 scopus 로고    scopus 로고
    • Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily
    • Narayanan B.C., Niu W., Han Y., Zou J., Mariano P.S., Dunaway-Mariano D., and Herzberg O. Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry 47 (2008) 167-182
    • (2008) Biochemistry , vol.47 , pp. 167-182
    • Narayanan, B.C.1    Niu, W.2    Han, Y.3    Zou, J.4    Mariano, P.S.5    Dunaway-Mariano, D.6    Herzberg, O.7
  • 7
    • 0037435596 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis ketopantoate hydroxymethyltransferase: tetrahydrofolate-independent hydroxymethyltransferase and enolization reactions with alpha-keto acids
    • Sugantino M., Zheng R., Yu M., and Blanchard J.S. Mycobacterium tuberculosis ketopantoate hydroxymethyltransferase: tetrahydrofolate-independent hydroxymethyltransferase and enolization reactions with alpha-keto acids. Biochemistry 42 (2003) 191-199
    • (2003) Biochemistry , vol.42 , pp. 191-199
    • Sugantino, M.1    Zheng, R.2    Yu, M.3    Blanchard, J.S.4
  • 8
    • 0032832111 scopus 로고    scopus 로고
    • Oxalic acid production by Aspergillus niger: an oxalate-non-producing mutant produces citric acid at pH 5 and in the presence of manganese
    • Ruijter G.J., van de Vondervoort P.J., and Visser J. Oxalic acid production by Aspergillus niger: an oxalate-non-producing mutant produces citric acid at pH 5 and in the presence of manganese. Microbiology 145 (1999) 2569-2576
    • (1999) Microbiology , vol.145 , pp. 2569-2576
    • Ruijter, G.J.1    van de Vondervoort, P.J.2    Visser, J.3
  • 9
    • 0029100574 scopus 로고
    • New protease mutants in Aspergillus niger result in strongly reduced in vitro degradation of target proteins; genetical and biochemical characterization of seven complementation groups
    • van den Hombergh J.P., van de Vondervoort P.J., van der Heijden N.C., and Visser J. New protease mutants in Aspergillus niger result in strongly reduced in vitro degradation of target proteins; genetical and biochemical characterization of seven complementation groups. Curr. Genet. 28 (1995) 299-308
    • (1995) Curr. Genet. , vol.28 , pp. 299-308
    • van den Hombergh, J.P.1    van de Vondervoort, P.J.2    van der Heijden, N.C.3    Visser, J.4
  • 10
    • 33846861493 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    • Pel H.J., de Winde J.H., Archer D.B., Dyer P.S., Hofmann G., Schaap P.J., et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat. Biotechnol. 25 (2007) 221-231
    • (2007) Nat. Biotechnol. , vol.25 , pp. 221-231
    • Pel, H.J.1    de Winde, J.H.2    Archer, D.B.3    Dyer, P.S.4    Hofmann, G.5    Schaap, P.J.6
  • 11
    • 29244445824 scopus 로고    scopus 로고
    • Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids
    • Lu Z., Feng X., Song L., Han Y., Kim A., Herzberg O., et al. Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids. Biochemistry 44 (2005) 16365-16376
    • (2005) Biochemistry , vol.44 , pp. 16365-16376
    • Lu, Z.1    Feng, X.2    Song, L.3    Han, Y.4    Kim, A.5    Herzberg, O.6
  • 12
    • 0019053306 scopus 로고
    • Relation between structure and function of alpha/beta-proteins
    • Branden C.I. Relation between structure and function of alpha/beta-proteins. Q. Rev. Biophys. 13 (1980) 317-338
    • (1980) Q. Rev. Biophys. , vol.13 , pp. 317-338
    • Branden, C.I.1
  • 13
    • 34248230247 scopus 로고    scopus 로고
    • Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi
    • Han Y., Joosten H.J., Niu W., Zhao Z., Mariano P.S., McCalman M., et al. Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi. J. Biol. Chem. 282 (2007) 9581-9590
    • (2007) J. Biol. Chem. , vol.282 , pp. 9581-9590
    • Han, Y.1    Joosten, H.J.2    Niu, W.3    Zhao, Z.4    Mariano, P.S.5    McCalman, M.6
  • 14
    • 0037414444 scopus 로고    scopus 로고
    • Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre
    • Grimm C., Evers A., Brock M., Maerker C., Klebe G., Buckel W., and Reuter K. Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre. J. Mol. Biol. 328 (2003) 609-621
    • (2003) J. Mol. Biol. , vol.328 , pp. 609-621
    • Grimm, C.1    Evers, A.2    Brock, M.3    Maerker, C.4    Klebe, G.5    Buckel, W.6    Reuter, K.7
  • 15
    • 0142090797 scopus 로고    scopus 로고
    • Crystal structure of Salmonella typhimurium 2-methylisocitrate lyase (PrpB) and its complex with pyruvate and Mg(2+)
    • Simanshu D.K., Satheshkumar P.S., Savithri H.S., and Murthy M.R. Crystal structure of Salmonella typhimurium 2-methylisocitrate lyase (PrpB) and its complex with pyruvate and Mg(2+). Biochem. Biophys. Res. Commun. 311 (2003) 193-201
    • (2003) Biochem. Biophys. Res. Commun. , vol.311 , pp. 193-201
    • Simanshu, D.K.1    Satheshkumar, P.S.2    Savithri, H.S.3    Murthy, M.R.4
  • 18
    • 37348999191 scopus 로고    scopus 로고
    • Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method
    • Joosten H.J., Han Y., Niu W., Vervoort J., Dunaway-Mariano D., and Schaap P.J. Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method. Proteins 70 (2008) 157-166
    • (2008) Proteins , vol.70 , pp. 157-166
    • Joosten, H.J.1    Han, Y.2    Niu, W.3    Vervoort, J.4    Dunaway-Mariano, D.5    Schaap, P.J.6
  • 20
    • 0041559746 scopus 로고    scopus 로고
    • Residues C123 and D58 of the 2-methylisocitrate lyase (PrpB) enzyme of Salmonella enterica are essential for catalysis
    • Grimek T.L., Holden H., Rayment I., and Escalante-Semerena J.C. Residues C123 and D58 of the 2-methylisocitrate lyase (PrpB) enzyme of Salmonella enterica are essential for catalysis. J. Bacteriol. 185 (2003) 4837-4843
    • (2003) J. Bacteriol. , vol.185 , pp. 4837-4843
    • Grimek, T.L.1    Holden, H.2    Rayment, I.3    Escalante-Semerena, J.C.4
  • 21
    • 0025002985 scopus 로고
    • Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors
    • Brady K., Wei A.Z., Ringe D., and Abeles R.H. Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors. Biochemistry 29 (1990) 7600-7607
    • (1990) Biochemistry , vol.29 , pp. 7600-7607
    • Brady, K.1    Wei, A.Z.2    Ringe, D.3    Abeles, R.H.4
  • 22
    • 0022746525 scopus 로고
    • Inhibition of serine proteases by peptidyl fluoromethyl ketones
    • Imperiali B., and Abeles R.H. Inhibition of serine proteases by peptidyl fluoromethyl ketones. Biochemistry 25 (1986) 3760-3767
    • (1986) Biochemistry , vol.25 , pp. 3760-3767
    • Imperiali, B.1    Abeles, R.H.2
  • 27
    • 0028240897 scopus 로고
    • A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server
    • Appel R.D., Bairoch A., and Hochstrasser D.F. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci. 19 (1994) 258-260
    • (1994) Trends Biochem. Sci. , vol.19 , pp. 258-260
    • Appel, R.D.1    Bairoch, A.2    Hochstrasser, D.F.3
  • 29
    • 0019171450 scopus 로고
    • Nicotinic acid metabolism enzymic preparation and absolute configuration of the substrate for 2,3-dimethylmalate lyase
    • Lill U., Pirzer P., Kukla D., Huber R., and Eggerer H. Nicotinic acid metabolism enzymic preparation and absolute configuration of the substrate for 2,3-dimethylmalate lyase. Hoppe-Seyler's Z. Physiol. Chem. 361 (1980) 875-884
    • (1980) Hoppe-Seyler's Z. Physiol. Chem. , vol.361 , pp. 875-884
    • Lill, U.1    Pirzer, P.2    Kukla, D.3    Huber, R.4    Eggerer, H.5
  • 30
    • 0017070142 scopus 로고
    • Partial purification and some properties of oxalacetase from Aspergillus niger
    • Lenz H., Wunderwald P., and Eggerer H. Partial purification and some properties of oxalacetase from Aspergillus niger. Eur. J. Biochem. 65 (1976) 225-236
    • (1976) Eur. J. Biochem. , vol.65 , pp. 225-236
    • Lenz, H.1    Wunderwald, P.2    Eggerer, H.3
  • 36
    • 0026597444 scopus 로고
    • Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
    • Brunger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472-475
    • (1992) Nature , vol.355 , pp. 472-475
    • Brunger, A.T.1
  • 37
    • 0035182073 scopus 로고    scopus 로고
    • Use of TLS parameters to model anisotropic displacements in macromolecular refinement
    • Winn M.D., Isupov M.N., and Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. (2001) 122-123
    • (2001) Acta Crystallogr. , pp. 122-123
    • Winn, M.D.1    Isupov, M.N.2    Murshudov, G.N.3
  • 39
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85 (1988) 2444-2448
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 40
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183 (1990) 63-98
    • (1990) Methods Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 41
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J. 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.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.