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Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.

Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D
Biochemistry 37 4958-67 (1998)
Cited: 37 times
EuropePMC logo PMID: 9538014

Abstract

The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.

Articles - 3daa mentioned but not cited (7)

  1. Glycoprotein composition along the pistil of Malus x domestica and the modulation of pollen tube growth. Losada JM, Herrero M. BMC Plant Biol 14 1 (2014)
  2. The substrate specificity, enantioselectivity and structure of the (R)-selective amine : pyruvate transaminase from Nectria haematococca. Sayer C, Martinez-Torres RJ, Richter N, Isupov MN, Hailes HC, Littlechild JA, Ward JM. FEBS J 281 2240-2253 (2014)
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  4. Crystallization and preliminary X-ray diffraction studies of the (R)-selective amine transaminase from Aspergillus fumigatus. Thomsen M, Skalden L, Palm GJ, Höhne M, Bornscheuer UT, Hinrichs W. Acta Crystallogr Sect F Struct Biol Cryst Commun 69 1415-1417 (2013)
  5. Expanding the Toolbox of R-Selective Amine Transaminases by Identification and Characterization of New Members. Telzerow A, Paris J, Håkansson M, González-Sabín J, Ríos-Lombardía N, Gröger H, Morís F, Schürmann M, Schwab H, Steiner K. Chembiochem 22 1232-1242 (2021)
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  7. To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Shilova SA, Khrenova MG, Matyuta IO, Nikolaeva AY, Rakitina TV, Klyachko NL, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY. Molecules 28 2109 (2023)


Reviews citing this publication (10)

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  2. Cytoplasmic steps of peptidoglycan biosynthesis. Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. FEMS Microbiol Rev 32 168-207 (2008)
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  6. Enantiocomplementary enzymes: classification, molecular basis for their enantiopreference, and prospects for mirror-image biotransformations. Mugford PF, Wagner UG, Jiang Y, Faber K, Kazlauskas RJ. Angew Chem Int Ed Engl 47 8782-8793 (2008)
  7. Construction of C-N bonds from small-molecule precursors through heterogeneous electrocatalysis. Li J, Zhang Y, Kuruvinashetti K, Kornienko N. Nat Rev Chem 6 303-319 (2022)
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Articles citing this publication (20)

  1. Catalysing new reactions during evolution: economy of residues and mechanism. Bartlett GJ, Borkakoti N, Thornton JM. J Mol Biol 331 829-860 (2003)
  2. Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli. Kawai Y, Ishii Y, Arakawa K, Uemura K, Saitoh B, Nishimura J, Kitazawa H, Yamazaki Y, Tateno Y, Itoh T, Saito T. Appl Environ Microbiol 70 2906-2911 (2004)
  3. Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin. Goto M, Miyahara I, Hirotsu K, Conway M, Yennawar N, Islam MM, Hutson SM. J Biol Chem 280 37246-37256 (2005)
  4. Pre-steady-state reaction of 5-aminolevulinate synthase. Evidence for a rate-determining product release. Hunter GA, Ferreira GC. J Biol Chem 274 12222-12228 (1999)
  5. Functional attributes of the phosphate group binding cup of pyridoxal phosphate-dependent enzymes. Denesyuk AI, Denessiouk KA, Korpela T, Johnson MS. J Mol Biol 316 155-172 (2002)
  6. Crystal structure of an (R)-selective ω-transaminase from Aspergillus terreus. Łyskowski A, Gruber C, Steinkellner G, Schürmann M, Schwab H, Gruber K, Steiner K. PLoS One 9 e87350 (2014)
  7. Cloning and functional characterization of Arabidopsis thaliana D-amino acid aminotransferase--D-aspartate behavior during germination. Funakoshi M, Sekine M, Katane M, Furuchi T, Yohda M, Yoshikawa T, Homma H. FEBS J 275 1188-1200 (2008)
  8. Crystallographic characterization of the (R)-selective amine transaminase from Aspergillus fumigatus. Thomsen M, Skalden L, Palm GJ, Höhne M, Bornscheuer UT, Hinrichs W. Acta Crystallogr D Biol Crystallogr 70 1086-1093 (2014)
  9. Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold. Pavkov-Keller T, Strohmeier GA, Diepold M, Peeters W, Smeets N, Schürmann M, Gruber K, Schwab H, Steiner K. Sci Rep 6 38183 (2016)
  10. First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for L-amino acids and R-amines. Boyko KM, Stekhanova TN, Nikolaeva AY, Mardanov AV, Rakitin AL, Ravin NV, Bezsudnova EY, Popov VO. Extremophiles 20 215-225 (2016)
  11. Human mitochondrial and cytosolic branched-chain aminotransferases are cysteine S-conjugate beta-lyases, but turnover leads to inactivation. Cooper AJ, Bruschi SA, Conway M, Hutson SM. Biochem Pharmacol 65 181-192 (2003)
  12. Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization. Isupov MN, Boyko KM, Sutter JM, James P, Sayer C, Schmidt M, Schönheit P, Nikolaeva AY, Stekhanova TN, Mardanov AV, Ravin NV, Bezsudnova EY, Popov VO, Littlechild JA. Front Bioeng Biotechnol 7 7 (2019)
  13. A high-throughput assay for screening L- or D-amino acid specific aminotransferase mutant libraries. Walton CJ, Chica RA. Anal Biochem 441 190-198 (2013)
  14. Continuous colorimetric screening assay for detection of d-amino acid aminotransferase mutants displaying altered substrate specificity. Barber JE, Damry AM, Calderini GF, Walton CJ, Chica RA. Anal Biochem 463 23-30 (2014)
  15. Exploring routes to stabilize a cationic pyridoxamine in an artificial transaminase: site-directed mutagenesis versus synthetic cofactors. Häring D, Lees MR, Banaszak LJ, Distefano MD. Protein Eng 15 603-610 (2002)
  16. Metabolic bifunctionality of Rv0812 couples folate and peptidoglycan biosynthesis in Mycobacterium tuberculosis. Black KA, Duan L, Mandyoli L, Selbach BP, Xu W, Ehrt S, Sacchettini JC, Rhee KY. J Exp Med 218 e20191957 (2021)
  17. Modulation of activity and substrate specificity by modifying the backbone length of the distant interdomain loop of D-amino acid aminotransferase. Gutierrez A, Yoshimura T, Fuchikami Y, Esaki N. Eur J Biochem 267 7218-7223 (2000)
  18. The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme. Bakunova AK, Nikolaeva AY, Rakitina TV, Isaikina TY, Khrenova MG, Boyko KM, Popov VO, Bezsudnova EY. Molecules 26 5053 (2021)
  19. Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens. Shilova SA, Matyuta IO, Petrova ES, Nikolaeva AY, Rakitina TV, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY. Int J Mol Sci 24 16194 (2023)
  20. Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum. Bezsudnova EY, Nikolaeva AY, Bakunova AK, Rakitina TV, Suplatov DA, Popov VO, Boyko KM. PLoS One 16 e0255098 (2021)


Related citations provided by authors (1)

  1. Crystal Structure of a D-Amino Acid Aminotransferase: How the Protein Controls Stereoselectivity. Sugio S, Petsko GA, Manning JM, Soda K, Ringe D Biochemistry 34 9661- (1995)

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