Dihydroorotase from Escherichia coli: Loop movement and cooperativity between subunits

Journal of Molecular Biology

Volumn 348, Issue 3, 2005, Pages 523-533

  Lee, Mihwa ^a   Chan, Camilla W ^a   Guss, J Mitchell ^a   Christopherson, Richard I ^a   Maher, Megan J ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Carbamyl aspartate; Cooperativity; Dihydroorotase; Dihydroorotate; Flexible loop

Indexed keywords

ARGININE; ASPARTIC ACID; ASPARTIC ACID DERIVATIVE; DIHYDROOROTASE; HISTIDINE; MEMBRANE PROTEIN; N CARBAMYLASPARTATE; PROTEIN SUBUNIT; UNCLASSIFIED DRUG;

ARTICLE; CONCENTRATION RESPONSE; CONFORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTALLIZATION; ENZYME SUBUNIT; ESCHERICHIA COLI; HYDROGEN BOND; KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; SURFACE PROPERTY;

EID: 17144372272     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.01.067     Document Type: Article

References (35)

1. M.W. Washabaugh, and K.D. Collins Dihydroorotase from Escherichia coli. Purification and characterization J. Biol. Chem. 259 1984 3293 3298
2. P.F. Coleman, D.P. Suttle, and G.R. Stark Purification from hamster cells of the multifunctional protein that initiates de novo synthesis of pyrimidine nucleotides J. Biol. Chem. 252 1977 6379 6385
3. J.P. Simmer, R.E. Kelly, A.G. Rinker Jr, B.H. Zimmermann, J.L. Scully, H. Kim, and D.R. Evans Mammalian dihydroorotase: nucleotide sequence, peptide sequences, and evolution of the dihydroorotase domain of the multifunctional protein CAD Proc. Natl Acad. Sci. USA 87 1990 174 178
4. N.K. Williams, R.J. Simpson, R.L. Moritz, Y. Peide, L. Crofts, and E. Minasian Location of the dihydroorotase domain within trifunctional hamster dihydroorotate synthetase Gene 94 1990 283 288
5. L. Holm, and C. Sander An evolutionary treasure: unification of a broad set of amidohydrolases related to urease Proteins: Struct. Funct. Genet. 28 1997 72 82
6. D.K. Wilson, F.B. Rudolph, and F.A. Quiocho Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations Science 252 1991 1278 1284
7. C. Fields, D. Brichta, M. Shepherdson, M. Farinha, and G. O'Donovan Phylogenetic analysis and classification of dihydroorotases: a complex history for a complex enzyme Paths to Pyrimidines 7 1999 49 62
8. M.J. Maher, D.T. Huang, J.M. Guss, C.A. Collyer, and R.I. Christopherson Crystallization of hamster dihydroorotase: involvement of a disulfide-linked tetrameric form Acta Crystallog. sect. D Biol. Crystallog. 59 2003 381 384
9. C. Purcarea, P. Martin, J.F. Vickrey, H.I. Guy, B.F. Edwards, and D.R. Evans Cloning, expression and preliminary X-ray analysis of the dihydroorotase from the hyperthermophilic eubacterium Aquifex aeolicus Acta Crystallog. sect. D Biol. Crystallog. 58 2002 154 156
10. J.B. Thoden, G.N. Phillips Jr, T.M. Neal, F.M. Raushel, and H.M. Holden Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center Biochemistry 40 2001 6989 6997
11. J.M. Yon, D. Perahia, and C. Ghelis Conformational dynamics and enzyme activity Biochimie 80 1998 33 42
12. M. Gerstein, A.M. Lesk, and C. Chothia Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739 6749
13. Z. Faming, B. Kobe, C.B. Stewart, W.J. Rutter, and E.J. Goldsmith Structural evolution of an enzyme specificity. The structure of rat carboxypeptidase A2 at 1.9-A resolution J. Biol. Chem. 266 1991 24606 24612
14. M. Gulotta, H. Deng, R.B. Dyer, and R.H. Callender Toward an understanding of the role of dynamics on enzymatic catalysis in lactate dehydrogenase Biochemistry 41 2002 3353 3363
15. A.N. Szilagyi, M. Ghosh, E. Garman, and M. Vas A 1.8 A resolution structure of pig muscle 3-phosphoglycerate kinase with bound MgADP and 3-phosphoglycerate in open conformation: new insight into the role of the nucleotide in domain closure J. Mol. Biol. 306 2001 499 511
16. D.L. Pompliano, A. Peyman, and J.R. Knowles Stabilization of a reaction intermediate as a catalytic device: definition of the functional role of the flexible loop in triosephosphate isomerase Biochemistry 29 1990 3186 3194
17. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan Stereochemistry of polypeptide chain configuration J. Mol. Biol. 7 1963 95 99
18. S. Jones, and J.M. Thornton Prediction of protein-protein interaction sites using patch analysis J. Mol. Biol. 272 1997 133 143
19. D.C. Brown, and K.D. Collins Dihydroorotase from Escherichia coli. Substitution of Co(II) for the active site Zn(II) J. Biol. Chem. 266 1991 1597 1604
20. T.K. Harris, and A.S. Mildvan High-precision measurement of hydrogen bond lengths in proteins by nuclear magnetic resonance methods Proteins: Struct. Funct. Genet. 35 1999 275 282
21. M. Okoniewska, T. Tanaka, and R.Y. Yada The role of the flap residue, threonine 77, in the activation and catalytic activity of pepsin A Protein Eng. 12 1999 55 61
22. N.K. Williams, M.K. Manthey, T.W. Hambley, S.I. O'Donoghue, M. Keegan, B.E. Chapman, and R.I. Christopherson Catalysis by hamster dihydroorotase: zinc binding, site-directed mutagenesis, and interaction with inhibitors Biochemistry 34 1995 11344 11352
23. J. Krungkrai, A. Cerami, and G.B. Henderson Pyrimidine biosynthesis in parasitic protozoa: purification of a monofunctional dihydroorotase from Plasmodium berghei and Crithidia fasciculata Biochemistry 29 1990 6270 6275
24. G.J. Kleywegt, J.Y. Zou, M. Kjeldgaard, and T.A. Jones Model building and computer graphics M.G. Rossmann E. Arnold International Tables for Crystallography vol. F 2001 Kluwer Academic Publishers Dordrecht 353 356
25. G.J. Kleywegt, and T.A. Jones Deletion, delineation, measurement and display of cavities in macromolecular structures Acta Crystallog. sect. D Biol. Crystallog. D50 1994 178 185
26. R.I. Christopherson, K.J. Schmalzl, E. Szabados, R.J. Goodridge, M.C. Harsanyi, and M.E. Sant Mercaptan and dicarboxylate inhibitors of hamster dihydroorotase Biochemistry 28 1989 463 470
27. D.T. Huang, M.A. Thomas, and R.I. Christopherson Divalent metal derivatives of the hamster dihydroorotase domain Biochemistry 38 1999 9964 9970
28. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
29. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, and R.W. Grossekunstleve Crystallography and nmr system - a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
30. M.D. Winn, M.N. Isupov, and G.N. Murshudov Use of TLS parameters to model anisotropic displacements in macromolecular refinement Acta Crystallog. sect. D 57 2001 122 133
31. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallog. sect. D 53 1997 240 255
32. T.A. Jones, J.Y. Zou, S.W. Cowan, and Kjeldgaard 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
33. D.M. van Aalten, R. Bywater, J.B. Findlay, M. Hendlich, R.W. Hooft, and G. Vriend PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules J. Comput. Aided Mol. Des. 10 1996 255 262
34. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291
35. R.W.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272