Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate

Journal of Biosciences

Volumn 32, Issue 2, 2007, Pages 1195-1206

  Simanshu, Dhirendra K ^a   Chittori, Sagar ^a   Savithri, H S ^a   Murthy, M R N ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Crystal structure; L threonine; Propionate metabolism; Structure function relationship

Indexed keywords

ENZYME; PHOSPHATE ACETYLTRANSFERASE; PROPIONIC ACID; THREONINE; THREONINE DEHYDRATASE;

AMINO ACID; ANOXIC CONDITIONS; BIOCHEMISTRY; DEGRADATION; ENZYME ACTIVITY;

CRYSTAL STRUCTURE; ENZYME DEGRADATION; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; REVIEW; SALMONELLA TYPHIMURIUM;

ESCHERICHIA COLI; SALMONELLA TYPHIMURIUM;

EID: 35348859006     PISSN: 02505991     EISSN: 02505991     Source Type: Journal    
DOI: 10.1007/s12038-007-0121-1     Document Type: Review

References (66)

1. Anthony R S and Spector L B 1970 A phosphoenzyme intermediary in acetate kinase action; J. Biol. Chem. 245 6739-6741
2. Becker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S and Volker Wagner A F 1999 Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase; Nat. Struct. Biol. 6 969-975
3. Becker A and Kabsch W 2002 X-ray structure of pyruvate formatelyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage; J. Biol. Chem. 277 40036-40042
4. Bhadra R and Datta P 1978 Allosteric inhibition and catabolite inactivation of purified biodegradative threonine dehydratase of Salmonella typhimurium; Biochemistry 17 1691-1699
5. 18O] triphosphate and the mechanistic consequences for the reactions catalyzed by glycerol kinase, hexokinase, pyruvate kinase, and acetate kinase; Biochemistry 18 3927-3933
6. Buss K A, Cooper D R, Ingram-Smith C, Ferry J G, Sanders D A and Hasson M S 2001 Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases; J. Bacteriol. 183 680-686
7. Chase T, Jr. and Rabinowitz J C 1968 Role of pyruvate and Sadenosylmethionine in activating the pyruvate formate-lyase of Escherichia coli; J. Bacteriol. 96 1065-1078
8. Chattopadhyay S, Wu Y, and Datta P 1997 Involvement of FNR and ArcA in anaerobic expression of the tdc operon of Escherichia coli; J. Bacteriol. 179 4868-4873
9. DeLano W L 2002 The PyMOL Molecular Graphics System (San Carlos, CA: DeLano Scientific)
10. Dunne C P and Wood W A 1975 L-threonine dehydrase as a model of allosteric control involving ligand-induced oligomerization; Curr. Top. Cell Regul. 9 65-101
11. Eisenstein E 1991 Cloning, expression, purification, and characterization of biosynthetic threonine deaminase from Escherichia coli; J. Biol. Chem. 266 5801-5807
12. Feldman D A and Datta P 1975 Catabolite inactivation of biodegradative threonine dehydratase of Escherichia coli; Biochemistry 14 1760-1767
13. 2H]glycine-substituted enzyme and peptides homologous to the glycine 734 site; J. Biol. Chem. 269 12432-12437
14. Galperin M Y and Grishin N V 2000 The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase; Proteins 41 238-247
15. Ganduri Y L, Sadda S R, Datta M W, Jambukeswaran R K and Datta P 1993 TdcA, a transcriptional activator of the tdcABC operon of Escherichia coli, is a member of the LysR family of proteins; Mol. Gen. Genet. 240 395-402
16. Gerlt J A, Rabinowitz K W, Dunne C P and Wood W A 1973 The mechanism of action of 5′-adenylic acid-activated threonine dehydrase. V. Relation between ligand-induced allosteric activation and the protomer-oligomer interconversion; J. Biol. Chem. 248 8200-8206
17. Gorrell A, Lawrence S H and Ferry J G 2005 Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila; J. Biol. Chem. 280 10731-10742
18. Hesslinger C, Fairhurst S A and Sawers G 1998 Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate; Mol. Microbiol. 27 477-492
19. Higgins D, Thompson J, Gibson T, Thompson J D, Higgins D G and Gibson T J 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice; Nucleic Acids Res. 22 4673-4680
20. Ingram-Smith C, Gorrell A, Lawrence S H, Iyer P, Smith K and Ferry J G 2005 Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate kinase; J. Bacteriol. 187 2386-2394
21. Iyer P P, Lawrence S H, Luther K B, Rajashankar K R, Yennawar H P, Ferry J G and Schindelin H 2004 Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila; Structure 12 559-567
22. Knappe J, Blaschkowski H P, Grobner P and Schmitt T 1974 Pyruvate formate-lyase of Escherichia coli: the acetyl-enzyme intermediate; Eur. J. Biochem. 50 253-263
23. Knappe J, Neugebauer F A, Blaschkowski H P and Ganzler M 1984 Post-translational activation introduces a free radical into pyruvate formate-lyase; Proc. Natl. Acad. Sci. USA 81 1332-1335
24. Lawrence S H and Ferry J G 2006 Steady-state kinetic analysis of phosphotransacetylase from Methanosarcina thermophila; J. Bacteriol. 188 1155-1158
25. Lawrence S H, Luther K B, Schindelin H and Ferry J G 2006 Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila; J. Bacteriol. 188 1143-1154
26. Lehtio L, Leppanen V M, Kozarich J W and Goldman A 2002 Structure of Escherichia coli pyruvate formate-lyase with pyruvate; Acta Crystallogr. D Biol. Crystallogr. 58 2209-2212
27. Luginbuhl G H, Hofler J G, Decedue C J and Burns R O 1974 Biodegradative L-threonine deaminase of Salmonella typhimurium; J. Bacteriol. 120 559-561
28. McCleary W R and Stock J B 1994 Acetyl phosphate and the activation of two-component response regulators; J. Biol. Chem. 269 31567-31572
29. McCleary W R, Stock J B and Ninfa A J 1993 Is acetyl phosphate a global signal in Escherichia coli?; J. Bacteriol. 175 2793-2798
30. Miles R D, Gorrell A and Ferry J G 2002 Evidence for a transition state analog, MgADP-aluminum fluoride-acetate, in acetate kinase from Methanosarcina thermophila; J. Biol. Chem. 277 22547-22552
31. Miles R D, Iyer P P and Ferry J G 2001 Site-directed mutational analysis of active site residues in the acetate kinase from Methanosarcina thermophila; J. Biol. Chem. 276 45059-45064
32. Monod J, Wyman J and Changeux J P 1965 On the nature of allosteric transitions: a plausible model; J. Mol. Biol. 12 88-118
33. Nakazawa A, Tokushige M, Hayaishi O, Ikehara M and Mizuno Y 1967 Studies on the interaction between regulatory enzymes and effectors. I. Effect of adenosine 5′-monophosphate analogues on threonine deaminase; J. Biol. Chem. 242 3868-3872
34. Park L S and Datta P 1979 Inhibition of Escherichia coli biodegradative threonine dehydratase by pyruvate; J. Bacteriol. 138 1026-1028
35. Pelroy R A and Whiteley H R 1972 Kinetic properties of phosphotransacetylase from Veillonella alcalescens; J. Bacteriol. 111 47-55.
36. Rabinowitz K W, Shada J D and Wood W A 1968 The mechanism of action of 5′-adenylic acid-activated threonine dehydratase. III. Structural requirements for nucleotide allosteric activation; J. Biol. Chem. 243 3214-3217
37. Rado T A and Hoch J A 1973 Phosphotransacetylase from Bacillus subtilis: purification and physiological studies; Biochim. Biophys. Acta 321 114-125
38. Sawers G 1998 The anaerobic degradation of L-serine and L-threonine in enterobacteria: networks of pathways and regulatory signals; Arch. Microbiol. 171 1-5
39. Sawers G 2001 A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon; Mol. Microbiol. 39 1285-1298
40. Sawers G, Hesslinger C, Muller N and Kaiser M 1998 The glycyl radical enzyme TdcE can replace pyruvate formate-lyase in glucose fermentation; J. Bacteriol. 180 3509-3516
41. Schweizer H P and Datta P 1989 Identification and DNA sequence of tdcR, a positive regulatory gene of the tdc operon of Escherichia coli; Mol. Gen. Genet. 218 516-522
42. Shimizu M, Suzuki T, Kameda K Y and Abiko Y 1969 Phosphotransacetylase of Escherichia coli B, purification and properties; Biochim. Biophys. Acta 191 550-558
43. Shizuta Y and Hayaishi O 1976 Regulation of biodegradative threonine deaminase; Curr. Top. Cell Regul. 11 99-146
44. Shizuta Y, Kurosawa A, Inoue K, Tanabe T and Hayaishi O 1973 Regulation of biodegradative threonine deaminase. I. Allosteric inhibition of the enzyme by a reaction product and its reversal by adenosine 5′-monophosphate; J. Biol. Chem. 248 512-520
45. Simanshu D K, Savithri H S and Murthy M R 2005 Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily; J. Mol. Biol. 352 876-892
46. Simanshu D K, Savithri H S and Murthy M R 2006 Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation; J. Biol. Chem. 281 39630-39641
47. 4A synthetic activity; Proteins (in press).
48. Spector L B 1980 Acetate kinase: a triple-displacement enzyme; Proc. Natl. Acad. Sci. USA 77 2626-2630
49. Suzuki T 1969 Phosphotransacetylase of Escherichia coli B, activation by pyruvate and inhibition by NADH and certain nucleotides; Biochim. Biophys. Acta 191 559-569
50. Suzuki T, Abiko Y and Shimizu M 1969 Activation and inhibition of purified phosphotransacetylase of Escherichia coli B by pyruvate and by NADH2 and certain nucleotides; Biochem. Biophys. Res. Commun. 35 102-108
51. Tokushige M, Whiteley H R and Hayaishi O 1963 Energy-linked regulation of threonine metabolism by ADP; Biochem. Biophys. Res. Commun. 27 380-385
52. Umbarger E and Brown B 1957 Threonine deamination in Escherichia coli II. Evidence for two L-threonine deaminases; J. Bacteriol. 73 105-112
53. Umbarger H E 1996 Biosynthesis of branched-chain amino acids; in Escherichia coli and Salmonella typhimurium: cellular and molecular biology (eds) F C Neidhardt, R Curtiss III, J L Ingraham, E C C Lin, K B Low, B Magasanik, W S Reznikoff, M Riley, M Schaechter, H E Umbarger et al (Washington DC: American Society for Microbiology Press) pp 442-457
54. Unkrig V, Neugebauer F A and Knappe J 1989 The free radical of pyruvate formate-lyase. Characterization by EPR spectroscopy and involvement in catalysis as studied with the substrate-analogue hypophosphite; Eur. J. Biochem. 184 723-728
55. Van Dyk T K and LaRossa R A 1987 Involvement of ack-pta operon products in alpha-ketobutyrate metabolism by Salmonella typhimurium; Mol. Gen. Genet. 207 435-440
56. 4-tetraphosphate: a pleiotropically acting alarmone? Cell 34 711-712
57. Wagner A F, Frey M, Neugebauer F A, Schafer W and Knappe J 1992 The free radical in pyruvate formate-lyase is located on glycine-734; Proc. Natl. Acad. Sci. USA 89 996-1000
58. Wanner B L and Wilmes-Riesenberg M R 1992 Involvement of phosphotransacetylase, acetate kinase, and acetyl phosphate synthesis in control of the phosphate regulon in Escherichia coli; J. Bacteriol. 174 2124-2130
59. Whanger P D, Phillips A T, Rabinowitz K W, Piperno J R, Shada J D and Wood W A 1968 The mechanism of action of 5′-adenylic acid-activated threonine dehydrase. II. Protomer-oligomer interconversions and related properties; J. Biol. Chem. 243 167-173
60. Wood W A and Gunsalus I C 1949 Serine and threonine deaminases of Escherichia coli: activators for a cell-free enzyme; J. Biol. Chem. 181 171-182
61. Wu Y F and Datta P 1992 Integration host factor is required for positive regulation of the tdc operon of Escherichia coli; J. Bacteriol. 174 233-240
62. Wu Y F, Patil R V and Datta P 1992 Catabolite gene activator protein and integration host factor act in concert to regulate tdc operon expression in Escherichia coli; J. Bacteriol. 174 6918-6927
63. Xu Q S, Shin D H, Pufan R, Yokota H, Kim R and Kim S H 2004 Crystal structure of a phosphotransacetylase from Streptococcus pyogenes; Proteins 55 479-481
64. Xu Q S, Jancarik J, Lou Y, Kuznetsova K, Yakunin A F, Yokota H, Adams P, Kim R and Kim S H 2005 Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate; J. Struct. Funct. Genomics 6 269-279
65. Yamada T, Komoto J, Takata Y, Ogawa H, Pitot H C and Takusagawa F 2003 Crystal structure of serine dehydratase from rat liver; Biochemistry 42 12854-12865
66. Zeng C and Fromm H J 1995 Active site residues of human brain hexokinase as studied by site-specific mutagenesis; J. Biol. Chem. 270 10509-10513