Structure of putrescine aminotransferase from Escherichia coli provides insights into the substrate specificity among class III aminotransferases

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Cha, Hyung Jin ^a   Jeong, Jae Hee ^a   Rojviriya, Catleya ^a   Kim, Yeon Gil ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOTRANSFERASE; DIAMINE; PUTRESCINE; PUTRESCINE AMINOTRANSFERASE; UNCLASSIFIED DRUG; YGJG ENZYME; PYRIDOXAL 5 PHOSPHATE;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DIMERIZATION; ENZYME BINDING; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBUNIT; ESCHERICHIA COLI; HYDROPHOBICITY; NONHUMAN; PROTEIN FOLDING; PROTEIN INTERACTION; SEQUENCE ANALYSIS; STEREOCHEMISTRY; STRUCTURE ANALYSIS; X RAY DIFFRACTION; AMINO ACID SEQUENCE; CHEMISTRY; ENZYMOLOGY; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN DENATURATION; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA COLI;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN DENATURATION; PUTRESCINE; PYRIDOXAL PHOSPHATE; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; TRANSAMINASES;

EID: 84912567709     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113212     Document Type: Article

References (35)

1. Tabor CW, Tabor H (1985) Polyamines in microorganisms. Microbiol Rev 49: 81-99.
2. Pegg AE (1986) Recent advances in the biochemistry of polyamines in eukaryotes. Biochem J 234: 249-262.
3. Linsalata M, Caruso MG, Leo S, Guerra V, D'Attoma B, et al. (2002) Prognostic value of tissue polyamine levels in human colorectal carcinoma. Anticancer Res 22: 2465-2469.
4. Boyle SM, MacIntyre MF, Sells BH (1977) Polyamine levels in Escherichia coli during nutritional shiftup and exponential growth. Biochim Biophys Acta 477: 221-227.
5. Poulin R, Pelletier G, Pegg AE (1995) Induction of apoptosis by excessive polyamine accumulation in ornithine decarboxylase-overproducing L1210 cells. Biochem J 311 (Pt 3): 723-727.
6. He Y, Kashiwagi K, Fukuchi J, Terao K, Shirahata A, et al. (1993) Correlation between the inhibition of cell growth by accumulated polyamines and the decrease of magnesium and ATP. Eur J Biochem 217: 89-96.
7. Wallace HM, Fraser AV, Hughes A (2003) A perspective of polyamine metabolism. Biochem J 376: 1-14.
8. Boyle SM, Markham GD, Hafner EW, Wright JM, Tabor H, et al. (1984) Expression of the cloned genes encoding the putrescine biosynthetic enzymes and methionine adenosyltransferase of Escherichia coli (speA, speB, speC and metK). Gene 30: 129-136.
9. Panagiotidis CA, Blackburn S, Low KB, Canellakis ES (1987) Biosynthesis of polyamines in ornithine decarboxylase, arginine decarboxylase, and agmatine ureohydrolase deletion mutants of Escherichia coli strain K-12. Proc Natl Acad Sci U S A 84: 4423-4427.
10. Kurihara S, Oda S, Kato K, Kim HG, Koyanagi T, et al. (2005) A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12. J Biol Chem 280: 4602-4608.
11. Kurihara S, Oda S, Tsuboi Y, Kim HG, Oshida M, et al. (2008) gamma-Glutamylputrescine synthetase in the putrescine utilization pathway of Escherichia coli K-12. J Biol Chem 283: 19981-19990.
12. Samsonova NN, Smirnov SV, Altman IB, Ptitsyn LR (2003) Molecular cloning and characterization of Escherichia coli K12 ygjG gene. BMC Microbiol 3: 2.
13. Samsonova NN, Smirnov SV, Novikova AE, Ptitsyn LR (2005) Identification of Escherichia coli K12 YdcW protein as a gamma-aminobutyraldehyde dehydrogenase. FEBS Lett 579: 4107-4112.
14. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-301.
15. Kim KH (1964) Purification and Properties of a Diamine Alpha-Ketoglutarate Transaminase from Escherichia Coli. J Biol Chem 239: 783-786.
16. Yeo SJ, Jeong JH, Yu SN, Kim YG (2012) Crystallization and preliminary X-ray crystallographic analysis of YgjG from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1070-1072.
17. Jeong JH, Kim YS, Rojvirija C, Cha HJ, Kim YG, et al. (2014) Structure of the hypothetical protein Ton 1535 from Thermococcus onnurineus NA1 reveals unique structural properties by a left-handed helical turn in normal alpha-solenoid protein. Proteins 82: 1072-1078.
18. Otwinowski Z MW (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
19. Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66: 22-25.
20. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
21. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
22. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26: 283-291.
23. Cha HJ, Jang DS, Kim YG, Hong BH, Woo JS, et al. (2013) Rescue of deleterious mutations by the compensatory Y30F mutation in ketosteroid isomerase. Mol Cells 36: 39-46.
24. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67: 235-242.
25. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
26. Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16: 10881-10890.
27. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31: 3320-3323.
28. Jansonius JN (1998) Structure, evolution and action of vitamin B6-dependent enzymes. Curr Opin Struct Biol 8: 759-769.
29. Schneider G, Kack H, Lindqvist Y (2000) The manifold of vitamin B6 dependent enzymes. Structure 8: R1-6.
30. Jortzik E, Fritz-Wolf K, Sturm N, Hipp M, Rahlfs S, et al. (2010) Redox regulation of Plasmodium falciparum ornithine delta-aminotransferase. J Mol Biol 402: 445-459.
31. Rausch C, Lerchner A, Schiefner A, Skerra A (2013) Crystal structure of the omega-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential. Proteins 81: 774-787.
32. Jager J, Moser M, Sauder U, Jansonius JN (1994) Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms. J Mol Biol 239: 285-305.
33. Storici P, Capitani G, Muller R, Schirmer T, Jansonius JN (1999) Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine. J Mol Biol 285: 297-309.
34. Hirotsu K, Goto M, Okamoto A, Miyahara I (2005) Dual substrate recognition of aminotransferases. Chem Rec 5: 160-172.
35. Liu W, Peterson PE, Carter RJ, Zhou X, Langston JA, et al. (2004) Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase. Biochemistry 43: 10896-10905.