Structural similarity between ornithine and aspartate transcarbamoylases of Escherichia coli: Characterization of the active site and evidence for an interdomain carboxy-terminal helix in ornithine transcarbamoylase

Protein Science

Volumn 5, Issue 4, 1996, Pages 709-718

  Murata, Lauren B ^a,b   Schachman, H K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b POMONA COLLEGE   (United States)

Author keywords

C terminal helix; Homology; Shared active sites; Structure prediction

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE; ORNITHINE CARBAMOYLTRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; THERMOSTABILITY;

AMINO ACID SEQUENCE; ASPARTATE CARBAMOYLTRANSFERASE; BINDING SITES; CALORIMETRY, DIFFERENTIAL SCANNING; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; KINETICS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; ORNITHINE CARBAMOYLTRANSFERASE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

EID: 0029920420     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050416     Document Type: Article

References (64)

1. Allewell NM. 1989. Escherichia coli aspartate transcarbamoylase: Structure, energetics, and catalytic and regulatory mechanisms. Annu Rev Biochem Biophys Chem 18:71-92.
2. Bencini DA, Houghton JE, Hoover TA, Foltermann KF, Wild JR, O'Donovan GA. 1983. The DNA sequence of argI from Escherichia coli K12. Nucleic Acids Res 11:8509-8518.
3. Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826.
4. Chou PY, Fasman GD. 1978. Empirical predictions of protein conformation. Annu Rev Biochem 47:251-276.
5. Davies GE, Vanaman TC, Stark GR. 1970. Aspartate transcarbamoylase. Stereospecific restrictions on the binding site for L-aspartate. J Biol Chem 245:1175-1179.
6. Devereux J, Haeberli P, Smithies O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387-395.
7. Edge V, Allewell NM, Sturtevant JM. 1985. High-resolution differential scanning calorimetric analysis of the subunits of Escherichia coli aspartate transcarbamoylase. Biochemistry 24:5899-5906.
8. Gerhart JC, Schachman HK. 1965. Distinct subunits for the regulation and catalytic activity of aspartate transcarbamoylase. Biochemistry 4:1054-1062.
9. Gigot D, Glansdorff N, Legrain C, Piérard A, Stalon V, Konisberg W, Caplier I, Strosberg AD, Hervé G. 1977. Comparison of the N-terminal sequences of aspartate and ornithine carbamoyltransferases of Escherichia coli. FEBS Lett 81:28-32.
10. Gouaux JE, Krause KL, Lipscomb WN. 1987. The catalytic mechanism of Escherichia coli aspartate transcarbamoylase: A molecular modelling study. Biochem Biophys Res Commun 142:893-897.
11. Gouaux JE, Lipscomb WN. 1988. Three-dimensional structure of carbamoyl phosphate and succinate bound to aspartate carbamoyltransferase. Proc Natl Acad Sci USA 85:4205-4208.
12. Honzatko RB, Crawford JL, Monaco HL, Ladner JE, Edwards BFP, Evans DR, Warren SG, Wiley DC, Ladner RC, Lipscomb WN. 1982. Crystal and molecular structures of native and CTP liganded aspartate carbamoyltransferase. J Mol Biol 160 219-263.
13. Hoogenraad NJ. 1978. Synthesis and properties of δ-N-(phosphonacetyl)-L-ornithine. A transition-state analog inhibitor of ornithine transcarbamylase. Arch Biochem Biophys 188:137-144.
14. Hoover TA, Roof WD, Foltermann GA, O'Donovan DA, Bencini DA, Wild JR. 1983. Nucleotide sequence of the structural gene (pyrB) that encodes the catalytic polypeptide of aspartate transcarbamoylase of Escherichia coli. Proc Natl Acad Sci USA 80:2462-2466.
15. Houghton J. 1986. Structural and functional comparisons between OTCase and ATCase, leading to the formation and characterization of an active "domain fusion" between argI (OTCase) and pyrB (ATCase) [thesis]. College Station, Texas: Texas A&M University.
16. Houghton JE, Bencini DA, O'Donovan G, Wild JR. 1984. Protein differentiation: A comparison of aspartate transcarbamoylase and ornithine transcarbamoylase from Escherichia coli K-12. Proc Natl Acad Sci USA 81:4864-4868.
17. Hsieh D. 1990. The role of serine-52 in the active site of aspartate transcarbamoylase [thesis]. Berkeley, California: University of California at Berkeley.
18. Kantrowitz ER, Lipscomb WN. 1990. Escherichia coli aspartate transcarbamoylase: The molecular basis for a concerted allosteric transition. Trends Biochem Sci 15:53-59.
19. Ke H, Lipscomb WN, Cho Y, Honzatko RB. 1988. Complex of N-phosphonacetyl-L-aspartate with aspartate carbamoyltransferase: X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms. J Mol Biol 204:725-747.
20. Kempe TD, Stark GR. 1975. Pyridoxal 5′-phosphate, a fluorescent probe in the active site of aspartate transcarbamoylase. J Biol Chem 250: 6861-6869.
21. Kim KH, Pan Z, Honzatko RB, Ke HM, Lipscomb WN. 1987. Structural asymmetry in the CTP-liganded form of aspartate carbamoyltransferase from Escherichia coli. J Mol Biol 196:853-875.
22. Kleanthous C, Wemmer DE, Schachman HK. 1988. The role of an active site histidine in the catalytic mechanism of aspartate transcarbamoylase. J Biol Chem 263:13062-13067.
23. Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
24. Krause KL, Volz KW, Lipscomb WN. 1987. 2.5 Å structure of aspartate carbamoyltransferase complexed with the bisubstrate analog N-(phosphonacetyl)-L-aspartate. J Mol Biol 193:527-553.
25. Kunkel TA, Roberts JD, Zakour RA. 1987. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol 154:367-382.
26. Kuo LC, Herzberg W, Lipscomb WN. 1985 Substrate specificity and protonation state of ornithine transcarbamoylase as determined by pH studies. Biochemistry 24:4754-4761.
27. Kuo LC, Lipscomb WN, Kantrowitz ER. 1982 Zn(II)-induced cooperativity of Escherichia coli ornithine transcarbamoylase. Proc Natl Acad Sci USA 79:2250-2254.
28. Kuo LC, Miller AW, Lee S, Kozuma C. 1988. Site-directed mutagenesis of Escherichia coli ornithine transcarbamoylase: Role of arginine-57 in substrate binding and catalysis. Biochemistry 27:8823-8832.
29. Legrain C, Halleux P, Stalon V, Glansdorff N. 1972. The dual genetic control of ornithine carbamoyltransferase in Escherichia coli: A case of bacterial hybrid enzymes. Eur J Biochem 27:93-102.
30. Legrain C, Stalon V, Noullez JP, Mercenier A, Simon JP, Broman K, Wiame JM. 1977. Structure and function of ornithine carbamoyltransferases. Eur J Biochem 80:401-409.
31. Lerner CG, Switzer RL. 1986. Cloning and structure of the Bacillus subtilis aspartate transcarbamylasegene (pyrB). J Biol Chem 261:11156-11165.
32. Marshall M, Cohen PP. 1972. Ornithine transcarbamylase from Streptococcus faecalis and bovine liver. I. Isolation and subunit structure. J Biol Chem 247:1641-1653.
33. Middleton SA, Stebbins JW, Kantrowitz ER. 1989. A loop involving catalytic chain residues 230-245 is essential for the stabilization of both allosteric forms of Escherichia coli aspartate transcarbamylase. Biochemistry 28:1617-1626.
34. Murata LB. 1994. Homology-based structural studies of Escherichia coli ornithine transcarbamoylase [thesis]. Berkeley, California: University of California at Berkeley.
35. Murata LB, Schachman HK. 1996. Structural similarity between ornithine and aspartate transcarbamoylases of Escherichia coli. Implications for domain switching. Protein Sci 5:719-728.
36. Peterson CB, Burman DL, Schachman HK. 1992. Effects of replacement of active site residue glutamine 231 on activity and allosteric properties of aspartate transcarbamoylase. Biochemistry 31:8508-8515.
37. Peterson CB, Schachman HK. 1991. Role of a carboxyl-terminal helix in the assembly, interchain interactions, and stability of aspartate transcarbamoylase. Proc Natl Acad Sci USA 88:458-462.
38. Peterson CB, Schachman HK. 1992. Long range effects of amino acid substitutions in the catalytic chain of aspartate transcarbamoylase. Localized replacements in the carboxyl-terminal α-helix cause marked alterations in allosteric properties and intersubunit interactions. J Biol Chem 267:2443-2450.
39. Peterson CB, Zhou BB, Hsieh D, Creager ANH, Schachman HK. 1994. Association of the catalytic subunit of aspartate transcarbamoylase with a zinc-containing polypeptide fragment of the regulatory chain leads to increases in thermal stability. Protein Sci 3:960-966.
40. Piette J, Cunin R, Van Vliet F, Charlier D, Crabeel M, Ota Y, Glansdorff N. 1982. Homologous control sites and DNA transcription starts in the related argF and argI genes of Escherichia coli K12. EMBO J 1:853-857.
41. Porter RW, Modebe MO, Stark GR. 1969. Aspartate transcarbamylase. Kinetic studies of the catalytic subunit. J Biol Chem 244:1846-1859.
42. Robey EA, Schachman HK. 1985. Regeneration of active enzyme by formation of hybrids from inactive derivatives: Implications for active sites shared between polypeptide chains of aspartate transcarbamoylase. Proc Natl Acad Sci USA 82:361-365.
43. Robey EA, Wente SR, Markby DW, Flint A, Yang YR, Schachman HK. 1986. Effect of amino acid substitutions on the catalytic and regulatory properties of aspartate transcarbamoylase. Proc Natl Acad Sci USA 83:5934-5938.
44. Roof WD, Foltermann KF, Wild JR. 1982. The organization and regulation of the pyrBI operon of E. coli includes a Rho-independent attenuator sequence. Mol Gen Genet 187:391-400.
45. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467.
46. Schachman HK. 1987. From allostery to mutagenesis: 20 years with aspartate transcarbamoylase. Biochem Soc Trans 15:772-775.
47. Schachman HK. 1993. Aspartate transcarbamoylase. Curr Opin Struct Biol 3:960-961.
48. Schachman HK, Pauza CD, Navre M, Karels MJ, Wu L, Yang YR. 1984. Location of amino acid alterations in mutants of aspartate transcarbamoylase: Structural aspects of interallelic complementation. Proc Natl Acad Sci USA 81:115-119.
49. Stebbins JW, Robenson DE, Roberts MF, Stevens RC, Lipscomb WN, Kantrowitz ER. 1992. Arginine 54 in the active site of Escherichia coli aspartate transcarbamoylase is critical for catalysis: A site-specific mutagenesis, NMR, and X-ray crystallographic study. Protein Sci 7:1435-1446.
50. Stebbins JW, Xu W, Kantrowitz ER. 1989. Three residues involved in binding and catalysis in the carbamoyl phosphate binding site of Escherichia coli aspartate transcarbamylase. Biochemistry 25:2592-2600.
51. Stebbins JW, Zhang Y, Kantrowitz ER. 1990. Importance of residues Arg-167 and Gln-231 in both the allosteric and catalytic mechanisms of Escherichia coli aspartate transcarbamoylase. Biochemistry 29:3821-3827.
52. Stevens RC, Cook YM, Cho CY, Lipscomb WN, Kantrowitz ER. 1991. Escherichia coli aspartate carbamoyltransferase: The probing of crystal structure analysis via site-specific mutagenesis. Protein Eng 4:391-408.
53. Tabor S. 1990. Expression using the T7 RNA polymerase/promoter system. In: Ausubel FA, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, eds. Current protocols in molecular biology. New York: Greene Publishing and Wiley-Interscience, pp 16.2.1-16.2.11.
54. Tabor S, Richardson CC. 1985. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci USA 82:1074-1078.
55. Van Vliet F, Cunin R, Jacobs A, Piette J, Gigot D, Lauwereys M, Pierard A, Glansdorff N. 1984. Evolutionary divergence of genes for ornithine and aspartate carbamoyl-transferases - Complete sequence and mode of regulation of the Escherichia coli argF gene; comparison of argF with argl and pyrB. Nucleic Acids Res 12:6277-6289.
56. Vickers LP, Donovan JW, Schachman HK. 1978. Differential scanning calorimetry of aspartate transcarbamoylase and its isolated subunits. J Biol Chem 253:8493-8498.
57. Villeret V, Tricot C, Stalon V, Dideberg O. 1995. 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 92:10762-10766.
58. Waldrop GL, Turnbull JL, Parmentier LE, Lee S, O'Leary MH, Cleland WW, Schachman HK. 1992a. The contribution of threonine 55 to catalysis in aspartate transcarbamoylase. Biochemistry 31:6592-6597.
59. Waldrop GL, Turnbull JL, Parmentier LE, O'Leary MH, Cleland WW, Schachman HK. 1992b. Steady-state kinetics and isotope effects on the mutant catalytic trimer of aspartate transcarbamoylase containing the replacement of histidine 134 by alanine. Biochemistry 31:6585-6591.
60. Wente SR. 1988. Site directed mutations altering the active site and the nucleotide-binding site of aspartate transcarbamoylase [thesis]. Berkeley, California: University of California at Berkeley.
61. Wente SR, Schachman HK. 1987. Shared active sites in oligomeric enzymes: Model studies with defective mutants of aspartate transcarbamoylase produced by site-directed mutagenesis. Proc Natl Acad Sci USA 84:31-35.
62. Xu W, Kantrowitz ER. 1991. Function of serine-52 and serine-80 in the catalytic mechanism of Escherichia coli aspartate transcarbamoylase. Biochemistry 30:2535-2542.
63. Yang YR, Kirschner MW, Schachman HK. 1978. Aspartate transcarbamoylase (Escherichia coli): Preparation of subunits. Methods Enzymol 51:35-41.
64. Yang YR, Schachman HK. 1987. Hybridization as a technique for studying interchain interactions in the catalytic trimers of aspartate transcarbamoylase. Anal Biochem 163:188-195.