The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction

Critical Reviews in Biochemistry and Molecular Biology
R E Viola

Abstract

The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?

References

Jun 1, 1990·Trends in Biochemical Sciences·G K Farber, Gregory A Petsko
Nov 1, 1971·Archives of Biochemistry and Biophysics·F B Rudolph, H J Fromm
Apr 15, 1984·Journal of Molecular Biology·J F KirschP Christen
Aug 1, 1984·Archives of Biochemistry and Biophysics·Frank M Raushel
Sep 16, 1980·Biochemistry·J S Blanchard, W W Cleland
Mar 1, 1995·Protein Science : a Publication of the Protein Society·J J Perona, C S Craik
Aug 1, 1993·Trends in Biochemical Sciences·R GrabowskiW Buckel
Oct 1, 1993·Trends in Biochemical Sciences·Gregory A PetskoJohn W Kozarich
Nov 1, 1996·The Journal of Biological Chemistry·J P Klinman
Jul 29, 1997·Biochemistry·W ShiG K Farber
Jul 17, 1998·Journal of Molecular Biology·T WeaverL Banaszak
Apr 1, 1999·Chemistry & Biology·P J O'Brien, D Herschlag
Oct 31, 2000·Journal of Molecular Biology·R R Copley, P Bork
Nov 9, 2000·Proceedings of the National Academy of Sciences of the United States of America·S UmhauS Ghisla
Feb 24, 2001·Proceedings of the National Academy of Sciences of the United States of America·D YarbroughS J Remington
Feb 14, 2002·Structure·Mathias Baedeker, Georg E Schulz
Apr 5, 2002·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·P Christen, P K Mehta
Jun 20, 2002·European Journal of Biochemistry·Dagmar RötherJános Rétey
Dec 12, 2002·Chemical Reviews·Lizbeth Hedstrom
Oct 22, 2003·Journal of Molecular Biology·Weidong Tian, Jeffrey Skolnick
May 25, 2004·The Journal of Biological Chemistry·Robert M CicchilloSquire J Booker
Oct 27, 2004·Acta Crystallographica. Section D, Biological Crystallography·Prasenjit BhaumikRik K Wierenga
Feb 4, 2005·Protein Science : a Publication of the Protein Society·Lei SunZihe Rao
Jun 3, 2005·Protein Science : a Publication of the Protein Society·Dirk KostrewaRemo Perozzo
Aug 13, 2005·The Journal of Biological Chemistry·Michaela MarkovaRobert A John
Mar 16, 2006·Journal of the American Chemical Society·Gregory J GattoChristopher T Walsh
Sep 22, 2006·The Journal of Biological Chemistry·Gregory A Grant
Dec 15, 2006·The Journal of Biological Chemistry·Annett KreimeyerJean Weissenbach
Dec 7, 2007·Journal of the American Chemical Society·Carl V ChristiansonSteven D Bruner
Mar 18, 2008·Archives of Biochemistry and Biophysics·Arthur J L CooperJeremy P E Spencer
Aug 30, 2008·Chemical Reviews·Thomas E MüllerMizuki Tada
Dec 17, 2009·PLoS Computational Biology·Alexandra M SchnoesPatricia C Babbitt
Jun 4, 2010·The Journal of Biological Chemistry·Naoki ShibataTetsuo Toraya
Dec 7, 2010·Current Opinion in Chemical Biology·Nicholas J Turner
Sep 1, 2011·Archives of Biochemistry and Biophysics·Xiao Lan XuGregory A Grant
Dec 27, 2011·Biochimica Et Biophysica Acta·Darya V UrusovaKlaus D Schnackerz
Dec 12, 2012·Biochemistry·Merlin Eric HobbsFrank M Raushel
Oct 1, 2013·ACS Chemical Biology·Alissa M GobleJohn E Cronan
Oct 15, 2013·Archives of Biochemistry and Biophysics·Michael D Toney
Jan 24, 2015·Biochimica Et Biophysica Acta·Robert S Phillips
Feb 28, 2015·Chemical Reviews·Liangbin HuangLukas J Gooßen
May 12, 2015·Current Protein & Peptide Science·Ranjith N KumavathVasco Azevedo
Sep 15, 2015·Biochemical and Biophysical Research Communications·Zhen QinZhengqiang Jiang
May 1, 2016·Nucleic Acids Research·Liisa Holm, Laura M Laakso
Dec 19, 2016·Applied Biochemistry and Biotechnology·Arti T PatelDarshan H Patel
May 13, 2017·Chemical Reviews·Fabio ParmeggianiNicholas J Turner
Dec 27, 2017·Biochimica Et Biophysica Acta. Proteins and Proteomics·Robert S PhillipsTimothy R Hoover
Jun 21, 2018·Biophysical Journal·Neslihan Ucuncuoglu, Kurt Warncke
Nov 18, 2018·Nucleic Acids Research·Arun Prasad PanduranganJulian Gough

Citations

Sep 8, 2018·Angewandte Chemie·Benjamin N Bhawal, Bill Morandi
Aug 28, 2020·Frontiers in Bioengineering and Biotechnology·Sergio Martínez-RodríguezEsperanza Ortega

Related Concepts

Ammonia-Lyases
Coenzymes
Sp1 Transcription Factor
Structure
Question (Inquiry)
Protein Function

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