M379A Mutant Tyrosine Phenol–lyase from Citrobacter freundii Has Altered Conformational Dynamics

Phillips, Robert S.; Jones, Benjamin; Nash, Sarah

doi:10.1002/cbic.202200028

Title: M379A Mutant Tyrosine Phenol–lyase from Citrobacter freundii Has Altered Conformational Dynamics

Journal Article · 23 May 2022 · ChemBioChem: a European journal of chemical biology

DOI: https://doi.org/10.1002/cbic.202200028 · OSTI ID:1877214

^[1]; Jones, Benjamin ^[1]; Nash, Sarah ^[1]

Univ. of Georgia, Athens, GA (United States)

The M379A mutant of Citrobacter freundii tyrosine phenol-lyase (TPL) has been prepared. M379A TPL is a robust catalyst to prepare a number of tyrosines substituted at the 3-position with bulky groups that cannot be made with wild type TPL. The three dimensional structures of M379A TPL complexed with L-methionine and 3-bromo-DL-phenylalanine have been determined by X-ray crystallography. Methionine is bound as a quinonoid complex in a closed active site in 3 of 4 chains of homotetrameric M379A TPL. M379A TPL reacts with L-methionine about 8-fold slower than wild type TPL. The temperature dependence shows that the slower reaction is due to less positive activation entropy. The structure of the M379A TPL complex of 3-bromo-DL-phenylalanine has a quinonoid complex in two subunits, with an open active site conformation. The effects of the M379A mutation on TPL suggest that the mutant enzyme has altered the conformational dynamics of the active site.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: W-31-109-ENG-3

OSTI ID:: 1877214

Journal Information:: ChemBioChem: a European journal of chemical biology, Journal Name: ChemBioChem: a European journal of chemical biology Journal Issue: 13 Vol. 23; ISSN 1439-4227

Publisher:: ChemPubSoc EuropeCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (34)

Cutting Long Syntheses Short: Access to Non-Natural Tyrosine Derivatives Employing an Engineered Tyrosine Phenol Lyase Seisser, Birgit; Zinkl, René; Gruber, Karl Advanced Synthesis & Catalysis, Vol. 352, Issue 4 https://doi.org/10.1002/adsc.200900826	journal	March 2010
Biocascade Synthesis of L-Tyrosine Derivatives by Coupling a Thermophilic Tyrosine Phenol-Lyase and L-Lactate Oxidase: Biocascade Synthesis of L-Tyrosine Derivatives by Coupling a Thermophilic Tyrosine Phenol-Lyase and L-Lactate Oxidase Li, Guosi; Lian, Jiazhang; Xue, Hailong European Journal of Organic Chemistry, Vol. 2020, Issue 8 https://doi.org/10.1002/ejoc.202000061	journal	February 2020
Reactions of O-acyl-l-serines with tryptophanase, tyrosine phenol-lyase, and tryptophan synthase Phillips, Robert S. Archives of Biochemistry and Biophysics, Vol. 256, Issue 1 https://doi.org/10.1016/0003-9861(87)90450-4	journal	July 1987
Enzymatic preparation of L-tyrosine and 3,4-dihydroxyphenyl-L-alanine Enei, Hitoshi; Matsui, Hiroshi; Okumura, Shinji Biochemical and Biophysical Research Communications, Vol. 43, Issue 6 https://doi.org/10.1016/S0006-291X(71)80021-9	journal	June 1971
Synthesis of L-tyrosine from pyruvate, ammonia and phenol by crystalline tyrosine phenol lyase Yamada, Hideaki; Kumagai, Hidehiko; Kashima, Nobukazu Biochemical and Biophysical Research Communications, Vol. 46, Issue 2 https://doi.org/10.1016/S0006-291X(72)80148-7	journal	January 1972
Tyrosine Phenol Lyase Kumagai, Hidehiko; Yamada, Hideaki; Matsui, Hiroshi Journal of Biological Chemistry, Vol. 245, Issue 7 https://doi.org/10.1016/S0021-9258(19)77158-0	journal	April 1970
Serine 51 residue of Citrobacter freundii tyrosine phenol-lyase assists in C-α-proton abstraction and transfer in the reaction with substrate Barbolina, Maria V.; Kulikova, Vitalia V.; Tsvetikova, Marina A. Biochimie, Vol. 147 https://doi.org/10.1016/j.biochi.2017.11.016	journal	April 2018
Change in heat capacity accurately predicts vibrational coupling in enzyme catalyzed reactions Arcus, Vickery L.; Pudney, Christopher R. FEBS Letters, Vol. 589, Issue 17 https://doi.org/10.1016/j.febslet.2015.06.042	journal	July 2015
Effective production of 3,4-dihydroxyphenyl-l-alanine (l-DOPA) with Erwinia herbicola cells carrying a mutant transcriptional regulator TyrR Koyanagi, Takashi; Katayama, Takane; Suzuki, Hideyuki Journal of Biotechnology, Vol. 115, Issue 3 https://doi.org/10.1016/j.jbiotec.2004.08.016	journal	February 2005
On the Temperature Dependence of Enzyme-Catalyzed Rates Arcus, Vickery L.; Prentice, Erica J.; Hobbs, Joanne K. Biochemistry, Vol. 55, Issue 12 https://doi.org/10.1021/acs.biochem.5b01094	journal	March 2016
Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism Phillips, Robert S.; Craig, Steven Biochemistry, Vol. 57, Issue 43 https://doi.org/10.1021/acs.biochem.8b00724	journal	September 2018
Biocatalytic One-Pot Synthesis of l -Tyrosine Derivatives from Monosubstituted Benzenes, Pyruvate, and Ammonia Dennig, Alexander; Busto, Eduardo; Kroutil, Wolfgang ACS Catalysis, Vol. 5, Issue 12 https://doi.org/10.1021/acscatal.5b02129	journal	November 2015
Ground-State Destabilization by Phe-448 and Phe-449 Contributes to Tyrosine Phenol-Lyase Catalysis Phillips, Robert S.; Vita, Andrew; Spivey, J. Blaine ACS Catalysis, Vol. 6, Issue 10 https://doi.org/10.1021/acscatal.6b01495	journal	September 2016
Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics Phillips, Robert S.; Craig, Steven; Kovalevsky, Andrey ACS Catalysis, Vol. 10, Issue 3 https://doi.org/10.1021/acscatal.9b03967	journal	December 2019
Site-Directed Mutagenesis of Tyrosine-71 to Phenylalanine in Citrobacter freundii Tyrosine Phenol-Lyase: Evidence for Dual Roles of Tyrosine-71 as a General Acid Catalyst in the Reaction Mechanism and in Cofactor Binding Chen, Hao Yuan; Demidkina, Tatyana V.; Phillips, Robert S. Biochemistry, Vol. 34, Issue 38 https://doi.org/10.1021/bi00038a023	journal	September 1995
Mechanistic deductions from kinetic isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: Erwinia herbicola and Citrobacter freundii tyrosine phenol-lyase Kiick, Dennis M.; Phillips, Robert S. Biochemistry, Vol. 27, Issue 19 https://doi.org/10.1021/bi00419a023	journal	September 1988
Hydrostatic Pressure Affects the Conformational Equilibrium of Salmonella typhimurium Tryptophan Synthase Phillips, Robert S.; Miles, Edith W.; Holtermann, Georg Biochemistry, Vol. 44, Issue 21 https://doi.org/10.1021/bi050056b	journal	May 2005
Crystallographic Snapshots of Tyrosine Phenol-lyase Show That Substrate Strain Plays a Role in C–C Bond Cleavage Milić, Dalibor; Demidkina, Tatyana V.; Faleev, Nicolai G. Journal of the American Chemical Society, Vol. 133, Issue 41 https://doi.org/10.1021/ja203361g	journal	October 2011
Significant improvement of oxidase activity through the genetic incorporation of a redox-active unnatural amino acid Yu, Yang; Zhou, Qing; Wang, Li Chemical Science, Vol. 6, Issue 7 https://doi.org/10.1039/C5SC01126D	journal	January 2015
Insights into the Catalytic Mechanism of Tyrosine Phenol-lyase from X-ray Structures of Quinonoid Intermediates Milić, Dalibor; Demidkina, Tatyana V.; Faleev, Nicolai G. Journal of Biological Chemistry, Vol. 283, Issue 43 https://doi.org/10.1074/jbc.M802061200	journal	August 2008
Stereoselective biocatalysis: A mature technology for the asymmetric synthesis of pharmaceutical building blocks Albarrán-Velo, Jesús; González-Martínez, Daniel; Gotor-Fernández, Vicente Biocatalysis and Biotransformation, Vol. 36, Issue 2 https://doi.org/10.1080/10242422.2017.1340457	journal	July 2017
Expanding the Use of Tyrosine Phenol Lyase in the Enzymatic Synthesis of Unnatural Amino Acids Munozvilla, Jubilee H.; Loo, Christian E.; Schwans, Jason P. The FASEB Journal, Vol. 34, Issue S1 https://doi.org/10.1096/fasebj.2020.34.s1.07582	journal	April 2020
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Syntheses of l-Tyrosine-Related Amino Acids by Tyrosine Phenol-lyase of Citrobacter intermedius Nagasawa, Toru; Utagawa, Takashi; Goto, Joji European Journal of Biochemistry, Vol. 117, Issue 1 https://doi.org/10.1111/j.1432-1033.1981.tb06299.x	journal	June 1981
Tyrosine phenol-lyase from Citrobacter intermedius: Factors controlling substrate specificity Faleev, Nikolai G.; Ruvinov, Sergei B.; Demidkina, Tatyana V. European Journal of Biochemistry, Vol. 177, Issue 2 https://doi.org/10.1111/j.1432-1033.1988.tb14387.x	journal	November 1988
Site-Directed Mutagenesis of His343Ala in Citrobacter freundii Tyrosine Phenol-Lyase. Effects on the Kinetic Mechanism and Rate-Determining Step Chen, Haoyuan; Gollnick, Paul; Phillips, Robert S. European Journal of Biochemistry, Vol. 229, Issue 2 https://doi.org/10.1111/j.1432-1033.1995.0540k.x	journal	April 1995
Effects of Tyrosine Ring Fluorination on Rates and Equilibria of Formation of Intermediates in the Reactions of Carbon-Carbon Lyases Phillips, Robert S.; Tersch, Robert L.; Secundo, Francesco European Journal of Biochemistry, Vol. 244, Issue 2 https://doi.org/10.1111/j.1432-1033.1997.00658.x	journal	March 1997
The mechanism of alpha-proton isotope exchange in amino acids catalysed by tyrosine phenol-lyase. What is the role of quinonoid intermediates? Faleev, Nicolai G.; Demidkina, Tatyana V.; Tsvetikova, Marina A. European Journal of Biochemistry, Vol. 271, Issue 22 https://doi.org/10.1111/j.1432-1033.2004.04428.x	journal	November 2004
Characterization of the "in vitro pulp chamber" using the cytotoxicity of phenol Hanks, C. T.; Diehl, M. L.; Craig, R. G. Journal of Oral Pathology and Medicine, Vol. 18, Issue 2 https://doi.org/10.1111/j.1600-0714.1989.tb00744.x	journal	February 1989
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012

Similar Records

Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism

Journal Article · 2018 · Biochemistry · OSTI ID:1483076

Phillips, Robert S.; Craig, Steven

Mechanistic deductions from kinetic isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: Erwinia herbicola and Citrobacter freundii tyrosine phenol-lyase

Journal Article · 1988 · Biochemistry; (United States) · OSTI ID:6354309

Kiick, D M; Phillips, R S

Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics

Journal Article · 2019 · ACS Catalysis · OSTI ID:1761712

Phillips, Robert S.; Craig, Steven; Kovalevsky, Andrey; +5 more

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
amino acids
biocatalysis
kinetics
mutagenesis
protein structures

Title: M379A Mutant Tyrosine Phenol–lyase from Citrobacter freundii Has Altered Conformational Dynamics

Citation Formats

References (34)

Similar Records

Related Subjects