First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for l-amino acids and R-amines
Tóm tắt
The gene TUZN1299 from the genome of the hyperthermophilic archaeon Thermoproteus uzoniensis encoding a new 32.8 kDa branched-chain amino acid aminotransferase (BCAT) was expressed in Escherichia coli. The recombinant protein TUZN1299 was purified to homogeneity in the PLP-bound form. TUZN1299 was active towards branched-chain amino acids (l-Val, l-Leu, l-Ile) and showed low but detectable activity toward (R)-alpha-methylbenzylamine. The enzyme exhibits high-temperature optimum, thermal stability, and tolerance to organic solvents. The structure of an archaeal BCAT called TUZN1299 was solved for the first time (at 2.0 Å resolution). TUZN1299 has a typical BCAT type IV fold, and the organization of its active site is similar to that of bacterial BCATs. However, there are some differences in the amino acid composition of the active site.
Tài liệu tham khảo
Bertrand SM et al (2015) The discovery of in vivo active mitochondrial branched-chain aminotransferase (BCATm) inhibitors by hybridizing fragment and HTS hits. J Med Chem. doi:10.1021/acs.jmedchem.5b00313
Boyko KM, Lipkin AV, Popov VO, Kovalchuk MV (2013) From gene to structure: the protein factory of the NBICS Centre of Kurchatov Institute. Crystallogr Rep+ 58:442–449. doi:10.1134/S106377451105004x
Castell A, Mille C, Unge T (2010) Structural analysis of mycobacterial branched-chain aminotransferase: implications for inhibitor design. Acta Crystallogr Sect D Biol Crystallogr 66:549–557. doi:10.1107/S0907444910004877
Chen CD et al (2012) Crystal structures of complexes of the branched-chain aminotransferase from Deinococcus radiodurans with alpha-ketoisocaproate and l-glutamate suggest the radiation resistance of this enzyme for catalysis. J Bacteriol 194:6206–6216. doi:10.1128/JB.01659-12
Collaborative Computational Project N (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr Sect D Biol Crystallogr 50:760–763. doi:10.1107/S0907444994003112
Diederichs K, Karplus PA (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4:269–275
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr Sect D Biol Crystallogr 66:486–501. doi:10.1107/S0907444910007493
Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr Sect D Biol Crystallogr 62:72–82. doi:10.1107/S0907444905036693
Goto M, Miyahara I, Hayashi H, Kagamiyama H, Hirotsu K (2003) Crystal structures of branched-chain amino acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme. Biochemistry 42:3725–3733. doi:10.1021/bi026722f
Grishin NV, Phillips MA, Goldsmith EJ (1995) Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci Publ Protein Soc 4:1291–1304. doi:10.1002/pro.5560040705
Hirotsu K, Goto M, Okamoto A, Miyahara I (2005) Dual substrate recognition of aminotransferases. Chem Record 5:160–172. doi:10.1002/tcr.20042
Hohne M, Schatzle S, Jochens H, Robins K, Bornscheuer UT (2010) Rational assignment of key motifs for function guides in silico enzyme identification. Nat Chem Biol 6:807–813. doi:10.1038/nchembio.447
Hooft RW, Sander C, Vriend G (1996) Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 26:363–376. doi:10.1002/(SICI)1097-0134(199612)26:4<363:AID-PROT1>3.0.CO;2-D
Hutson S (2001) Structure and function of branched-chain aminotransferases. Prog Nucl Acid Res Mol Biol 70:175–206
Jansonius JN (1998) Structure, evolution and action of vitamin B6-dependent enzymes. Curr Opin Struct Biol 8:759–769
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucl Acids Res 36:W5–W9. doi:10.1093/nar/gkn201
Kabsch W (2010) Xds. Acta Crystallogr Sect D Biol Crystallogr 66:125–132. doi:10.1107/S0907444909047337
Kochhar S, Christen P (1992) Mechanism of racemization of amino acids by aspartate aminotransferase. Eur J Biochem/FEBS 203:563–569
Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr Sect D Biol Crystallogr 60:2256–2268. doi:10.1107/S0907444904026460
Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797. doi:10.1016/j.jmb.2007.05.022
Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51:2778–2786. doi:10.1021/ci200227u
Mardanov AV, Gumerov VM, Beletsky AV, Prokofeva MI, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG (2011) Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20. J Bacteriol 193:3156–3157. doi:10.1128/JB.00409-11
Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491–497
Okada K, Hirotsu K, Sato M, Hayashi H, Kagamiyama H (1997) Three-dimensional structure of Escherichia coli branched-chain amino acid aminotransferase at 2.5 A resolution. J Biochem 121:637–641
Okada K, Hirotsu K, Hayashi H, Kagamiyama H (2001) Structures of Escherichia coli branched-chain amino acid aminotransferase and its complexes with 4-methylvalerate and 2-methylleucine: induced fit and substrate recognition of the enzyme. Biochemistry 40:7453–7463
Padilla JE, Yeates TO (2003) A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogra Sect D Biol Crystallogr 59:1124–1130
Pei J, Kim BH, Grishin NV (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucl Acids Res 36:2295–2300. doi:10.1093/nar/gkn072
Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D (1998) Crystallographic study of steps along the reaction pathway of d-amino acid aminotransferase. Biochemistry 37:4958–4967. doi:10.1021/bi972884d
Punta M et al (2012) The Pfam protein families database. Nucl Acids Res 40:D290–D301. doi:10.1093/nar/gkr1065
Siddiqui KS, Thomas T (2008) Protein adaptation in extremophiles. Nova Biomedical Books, New York
Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G (2015) A series of PDB-related databanks for everyday needs. Nucl Acids Res 43:D364–D368. doi:10.1093/nar/gku1028
Tremblay LW, Blanchard JS (2009) The 1.9 A structure of the branched-chain amino-acid transaminase (IlvE) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1071–1077. doi:10.1107/S1744309109036690
Uchida Y, Hayashi H, Washio T, Yamasaki R, Kato S, Oikawa T (2014) Cloning and characterization of a novel fold-type I branched-chain amino acid aminotransferase from the hyperthermophilic archaeon Thermococcus sp. CKU-1. Extremophiles 18:589–602. doi:10.1007/s00792-014-0642-0
Yennawar N, Dunbar J, Conway M, Hutson S, Farber G (2001) The structure of human mitochondrial branched-chain aminotransferase. Acta Crystallogr Sect D Biol Crystallogr 57:506–515
Yoshimura T, Nishimura K, Ito J, Esaki N, Kagamiyama H, Manning JM, Soda K (1993) Unique stereospecificity of d-amino-acid aminotransferase and branched-chain l-amino-acid aminotransferase for C-4′ hydrogen-transfer of the coenzyme. J Am Chem Soc 115:3897–3900. doi:10.1021/Ja00063a007