Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (βα)8 phosphoenolpyruvate/pyruvate superfamily

Journal of Bacteriology

Volumn 185, Issue 14, 2003, Pages 4163-4171

  Schmitzberger, Florian ^a   Smith, Alison G ^b   Abell, Chris ^a   Blundell, Tom L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Department of Plant Sciences ^*  (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOPANTOATE HYDROXYMETHYLTRANSFERASE; METHYLTRANSFERASE; PANTOTHENIC ACID; PHOSPHOENOLPYRUVATE; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; BACTERIUM IDENTIFICATION; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ESCHERICHIA COLI; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS; X RAY ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLIZATION; ESCHERICHIA COLI; HYDROXYMETHYL AND FORMYL TRANSFERASES; ISOCITRATE LYASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOSPHOENOLPYRUVATE; PHOSPHOTRANSFERASES (PHOSPHOMUTASES); PROTEIN CONFORMATION; PROTEIN FOLDING; PYRUVIC ACID;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0038154066     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.14.4163-4171.2003     Document Type: Article

References (30)

1. Britton, K. L., S. Langridge, P. J. Baker, K. Weeradechapon, S. E. Sedelnikova, J. R. De Lucas, D. W. Rice, and G. Turner. 2000. The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans. Structure 8:349-362.
2. Britton, K. L., I. S. Abeysinghe, P. J. Baker, V. Barynin, P. Diehl, S. J. Langridge, B. A. McFadden, S. E. Sedelnikova, T. J. Stillman, K. Weeradechapon, and D. W. Rice. 2001. The structure and domain organization of Escherichia coli isocitrate lyase. Acta Crystallogr. Sect. D 57:1209-1218.
3. Brown, G. M., and J. M. Williamson. 1982. Biosynthesis of riboflavin, folic acid, thiamine, and pantothenic acid. Adv. Enzymol. Relat. Areas Mol. Biol. 53:345-381.
4. Dreyer, M. K., and G. E. Schulz. 1996. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J. Mol. Biol. 259:458-466.
5. Hall, D. R., C. S. Bond, G. A. Leonard, C. I. Watt, A. Berry, and W. N. Hunter. 2002. Structure of tagatose-1,6-bisphosphate aldolase. Insight into chiral discrimination, mechanism, and specificity of class 11 aldolases. J. Biol. Chem. 277:22018-22024.
6. Hall, D. R., G. A. Leonard, C. D. Reed, C. I. Watt, A. Berry, and W. N. Hunter. 1999. The crystal structure of Escherichia coli class II fructose-1,6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J. Mol. Biol. 287:383-394.
7. Herzberg, O., C. C. Chen, G. Kapadia, M. McGuire, L. J. Carroll, S. J. Noh, and D. Dunaway-Mariano. 1996. Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Proc. Natl. Acad. Sci. USA 93:2652-2657.
8. Herzberg, O., C. C. Chen, S. Liu, A. Tempczyk, A. Howard, M. Wei, D. Ye, and D. Dunaway-Mariano. 2002. Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis. Biochemistry 41:780-787.
9. Holm, L., and C. Sander. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138.
10. 2+-oxalate. Struct. Fold. Des. 7:539-548.
11. Izard, T., and N. C. Blackwell. 2000. Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism. EMBO J. 19:3849-3856.
12. Kai, Y., H. Matsumura, T. Inoue, K. Terada, Y. Nagara, T. Yoshinaga, A. Kihara, K. Tsumura, and K. Izui. 1999. Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition. Proc. Natl. Acad. Sci. USA 96:823-828.
13. Keefe, A. D., G. L. Newton, and S. L. Miller. 1995. A possible prebiotic synthesis of pantetheine, a precursor to coenzyme A. Nature 373:683-685.
14. Kelley, L. A., R. M. MacCallum, and M. J. Sternberg. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299:499-520.
15. Kim, J., and D. Dunaway-Mariano. 1996. Phosphoenolpyruvate mutase catalysis of phosphoryl transfer in phosphoenolpyruvate: kinetics and mechanism of phosphorus-carbon bond formation. Biochemistry 35:4628-4635.
16. Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
17. 2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 Å resolution: ATP binding over a barrel. Biochemistry 37:6247-6255.
18. Luo, Y., J. Samuel, S. C. Mosimann, J. E. Lee, M. E. Tanner, and N. C. Strynadka. 2001. The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization. Biochemistry 40:14763-14771.
19. 2+-bound phosphoenolpyruvate carboxylase from Escherichia coli. FEBS Lett. 458:93-96.
20. Mattevi, A., G. Valentini, M. Rizzi, M. L. Speranza, M. Bolognesi, and A. Coda. 1995. Crystal structure of Escherichia coli pyruvate kinase type I: molecular basis of the allosteric transition. Structure 3:729-741.
21. Merritt, E. A., and D. J. Bacon. 1997. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:505-524.
22. Mizuguchi, K., C. M. Deane, T. L. Blundell, M. S. Johnson, and J. P. Overington. 1998. JOY: protein sequence-structure representation and analysis. Bioinformatics 14:617-623.
23. Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
24. Plater, A. R., S. M. Zgiby, G. J. Thomson, S. Qamar, C. W. Wharton, and A. Berry. 1999. Conserved residues in the mechanism of the E. coli class II FBP-aldolase. J. Mol. Biol. 285:843-855.
25. Saii, A., J. P. Overington, M. S. Johnson, and T. L. Blundell. 1990. From comparisons of protein sequences and structures to protein modelling and design. Trends Biochem. Sci. 15:235-240.
26. Sharma, V., S. Sharma, K. Hoener zu Bentrup, J. D. McKinney, D. G. Russell, W. R. Jacobs, Jr., and J. C. Sacchettini. 2000. Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat. Struct. Biol. 7:663-668.
27. Shi, J., T. L. Blundell, and K. Mizuguchi. 2001. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310:243-257.
28. Sutcliffe, M. J., I. Haneef, D. Carney, and T. L. Blundell. 1987. Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1:377-384.
29. Teichmann, S. A., S. C. Rison, J. M. Thornton, M. Riley, J. Gough, and C. Chothia. 2001. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311:693-708.
30. von Delft, F., T. Inoue, S. A. Saldanha, H. O. Ottenhof, F. Schmitzberger, L. M. Birch, V. Dhanaraj, M. Witty, A. G. Smith, T. L. Blundell, and C. Abell. Structure, in press.