Structural Insight into Substrate Selectivity of Erwinia chrysanthemi L-Asparaginase

Nguyen, Hien Anh; Su, Ying; Lavie, Arnon

doi:10.1021/acs.biochem.5b01351

Structural Insight into Substrate Selectivity of Erwinia chrysanthemi L-Asparaginase

Journal Article · Tue Feb 16 23:00:00 EST 2016 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.5b01351· OSTI ID:1247365

Nguyen, Hien Anh ^[1]; Su, Ying ^[1]; Lavie, Arnon ^[1]

The Jesse Brown VA Medical Center, Chicago, IL (United States); Univ. of Chicago, IL (United States)

L-Asparaginases of bacterial origin are a mainstay of acute lymphoblastic leukemia treatment. The mechanism of action of these enzyme drugs is associated with their capacity to deplete the amino acid L-asparagine from the blood. However, clinical use of bacterial L-asparaginases is complicated by their dual L-asparaginase and L-glutaminase activities. The latter, even though representing only ~10% of the overall activity, is partially responsible for the observed toxic side effects. Hence, L-asparaginases devoid of L-glutaminase activity hold potential as safer drugs. Understanding the key determinants of L-asparaginase substrate specificity is a prerequisite step toward the development of enzyme variants with reduced toxicity. Here we present crystal structures of the Erwinia chrysanthemi L-asparaginase in complex with L-aspartic acid and with L-glutamic acid. These structures reveal two enzyme conformations—open and closed—corresponding to the inactive and active states, respectively. The binding of ligands induces the positioning of the catalytic Thr15 into its active conformation, which in turn allows for the ordering and closure of the flexible N-terminal loop. Notably, L-aspartic acid is more efficient than L-glutamic acid in inducing the active positioning of Thr15. Structural elements explaining the preference of the enzyme for L-asparagine over L-glutamine are discussed with guidance to the future development of more specific L-asparaginases.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: National Institutes of Health (NIH); US Department of Veterans Affairs (VA)

OSTI ID:: 1247365

Journal Information:: Biochemistry, Journal Name: Biochemistry Journal Issue: 8 Vol. 55; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (39)

Glutaminase-free asparaginase fromvibrio succinogenes: An antilymphoma enzyme lacking hepatotoxicity Distasio, John A.; Salazar, Ana M.; Nadji, Mehrdad International Journal of Cancer, Vol. 30, Issue 3 https://doi.org/10.1002/ijc.2910300314	journal	September 1982
Reduced antithrombin III levels during L-asparaginase therapy Buchanan, George R.; Holtkamp, Christine A. Medical and Pediatric Oncology, Vol. 8, Issue 1 https://doi.org/10.1002/mpo.2950080103	journal	January 1980
Kinetic properties and inhibition of Acinetobacter glutaminase-asparaginase Steckel, Joph; Roberts, Joseph; Philips, Frederick S. Biochemical Pharmacology, Vol. 32, Issue 6 https://doi.org/10.1016/0006-2952(83)90613-5	journal	March 1983
A left-handed crossover involved in amidohydrolase catalysis: Crystal structure of Miller, Maria; Rao, J. K. Mohana; Wlodawer, Alexander FEBS Letters, Vol. 328, Issue 3 https://doi.org/10.1016/0014-5793(93)80943-o	journal	August 1993
Helicobacter pyloril-asparaginase: A promising chemotherapeutic agent Cappelletti, Donata; Chiarelli, Laurent R.; Pasquetto, Maria Valentina Biochemical and Biophysical Research Communications, Vol. 377, Issue 4 https://doi.org/10.1016/j.bbrc.2008.10.118	journal	December 2008
Purification and characterization of glutaminase-free l-asparaginase from Pectobacterium carotovorum MTCC 1428 Kumar, Sanjay; Venkata Dasu, V.; Pakshirajan, K. Bioresource Technology, Vol. 102, Issue 2 https://doi.org/10.1016/j.biortech.2010.07.114	journal	January 2011
Pharmacological and clinical evaluation of l-asparaginase in the treatment of leukemia Narta, Umesh K.; Kanwar, Shamsher S.; Azmi, Wamik Critical Reviews in Oncology/Hematology, Vol. 61, Issue 3 https://doi.org/10.1016/j.critrevonc.2006.07.009	journal	March 2007
Glutaminase activity determines cytotoxicity of l-asparaginases on most leukemia cell lines Parmentier, Jean Hugues; Maggi, Maristella; Tarasco, Erika Leukemia Research, Vol. 39, Issue 7 https://doi.org/10.1016/j.leukres.2015.04.008	journal	July 2015
Structural Basis for the Activity and Substrate Specificity of Erwinia chrysanthemi l -Asparaginase ^† ^, ^‡ Aghaiypour, Khosrow; Wlodawer, Alexander; Lubkowski, Jacek Biochemistry, Vol. 40, Issue 19 https://doi.org/10.1021/bi0029595	journal	May 2001
Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy. Swain, A. L.; Jaskolski, M.; Housset, D. Proceedings of the National Academy of Sciences, Vol. 90, Issue 4 https://doi.org/10.1073/pnas.90.4.1474	journal	February 1993
Identification and Structural Analysis of an l-Asparaginase Enzyme from Guinea Pig with Putative Tumor Cell Killing Properties Schalk, Amanda M.; Nguyen, Hien-Anh; Rigouin, Coraline Journal of Biological Chemistry, Vol. 289, Issue 48 https://doi.org/10.1074/jbc.m114.609552	journal	October 2014
Role of Glutamine Depletion in Directing Tissue-specific Nutrient Stress Responses to L-Asparaginase Reinert, Rachel B.; Oberle, L. Morgan; Wek, Sheree A. Journal of Biological Chemistry, Vol. 281, Issue 42 https://doi.org/10.1074/jbc.m604511200	journal	August 2006
In silico Engineering of L-Asparaginase to Have Reduced Glutaminase Side Activity for Effective Treatment of Acute Lymphoblastic Leukemia Ln, Ramya; Doble, Mukesh; Rekha, V. P. B. Journal of Pediatric Hematology/Oncology, Vol. 33, Issue 8 https://doi.org/10.1097/mph.0b013e31822aa4ec	journal	January 2011
MOLREP an Automated Program for Molecular Replacement Vagin, A.; Teplyakov, A. Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025 https://doi.org/10.1107/s0021889897006766	journal	December 1997
Structures of two highly homologous bacterial L -asparaginases: a case of enantiomorphic space groups Jaskólski, Mariusz; Kozak, Maciej; Lubkowski, Jacek Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 3 https://doi.org/10.1107/s0907444900020175	journal	March 2001
Atomic resolution structure of Erwinia chrysanthemi L -asparaginase Lubkowski, Jacek; Dauter, Miroslawa; Aghaiypour, Khosrow Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 1 https://doi.org/10.1107/s0907444902019443	journal	December 2002
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/s0907444909047374	journal	January 2010
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/s0907444996012255	journal	May 1997
Engineering the substrate specificity of Escherichia coli asparaginase II. Selective reduction of glutaminase activity by amino acid replacements at position 248 Derst, Christian; Henseling, Johannes; Röhm, Klaus-Heinrich Protein Science, Vol. 9, Issue 10 https://doi.org/10.1110/ps.9.10.2009	journal	January 2000
States and Functions of Tyrosine Residues in Escherichia coli Asparaginase II Derst, Christian; Wehner, Andreas; Specht, Volker European Journal of Biochemistry, Vol. 224, Issue 2 https://doi.org/10.1111/j.1432-1033.1994.00533.x	journal	September 1994
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Structural aspects of L-asparaginases, their friends and relations. Michalska, Karolina; Jaskolski, Mariusz Acta Biochimica Polonica, Vol. 53, Issue 4 https://doi.org/10.18388/abp.2006_3291	journal	December 2006
L-asparaginase for treatment of childhood acute lymphoblastic leukemia: What have we learned? (Commentary on Schrey et al., page 378) Asselin, Barbara L. Pediatric Blood & Cancer, Vol. 57, Issue 3 https://doi.org/10.1002/pbc.23135	journal	April 2011
A left-handed crossover involved in amidohydrolase catalysis: Crystal structure of Miller, Maria; Rao, J. K. Mohana; Wlodawer, Alexander FEBS Letters, Vol. 328, Issue 3 https://doi.org/10.1016/0014-5793(93)80943-O	journal	August 1993
Purification and properties of a highly potent antitumor glutaminase-asparaginase from Pseudomonas 7Z. Roberts, J. Journal of Biological Chemistry, Vol. 251, Issue 7 https://doi.org/10.1016/S0021-9258(17)33664-5	journal	April 1976
Dynamics of a mobile loop at the active site of Escherichia coli asparaginase Aung, Hnin-Pwint; Bocola, Marco; Schleper, Stefan Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1481, Issue 2 https://doi.org/10.1016/S0167-4838(00)00179-5	journal	September 2000
Ion Binding Induces Closed Conformation in Pseudomonas 7A Glutaminase-Asparaginase (PGA): Crystal Structure of the PGA-SO ₄ ^2- -NH ₄ ⁺ Complex at 1.7 Å Resolution ^† ^, ^‡ Jakob, Clarissa G.; Lewinski, Krzysztof; LaCount, Michael W. Biochemistry, Vol. 36, Issue 4 https://doi.org/10.1021/bi961979x	journal	January 1997
Identification and Structural Analysis of an l-Asparaginase Enzyme from Guinea Pig with Putative Tumor Cell Killing Properties Schalk, Amanda M.; Nguyen, Hien-Anh; Rigouin, Coraline Journal of Biological Chemistry, Vol. 289, Issue 48 https://doi.org/10.1074/jbc.M114.609552	journal	October 2014
Role of Glutamine Depletion in Directing Tissue-specific Nutrient Stress Responses to L-Asparaginase Reinert, Rachel B.; Oberle, L. Morgan; Wek, Sheree A. Journal of Biological Chemistry, Vol. 281, Issue 42 https://doi.org/10.1074/jbc.M604511200	journal	August 2006
Evidence that the L-Asparaginase of Guinea pig Serum is Responsible for its Antilymphoma Effects Broome, J. D. Journal of Experimental Medicine, Vol. 118, Issue 1 https://doi.org/10.1084/jem.118.1.99	journal	July 1963
In silico Engineering of L-Asparaginase to Have Reduced Glutaminase Side Activity for Effective Treatment of Acute Lymphoblastic Leukemia Ln, Ramya; Doble, Mukesh; Rekha, V. P. B. Journal of Pediatric Hematology/Oncology, Vol. 33, Issue 8 https://doi.org/10.1097/MPH.0b013e31822aa4ec	journal	January 2011
MOLREP an Automated Program for Molecular Replacement Vagin, A.; Teplyakov, A. Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025 https://doi.org/10.1107/S0021889897006766	journal	December 1997
Structures of two highly homologous bacterial L -asparaginases: a case of enantiomorphic space groups Jaskólski, Mariusz; Kozak, Maciej; Lubkowski, Jacek Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 3 https://doi.org/10.1107/S0907444900020175	journal	March 2001
Atomic resolution structure of Erwinia chrysanthemi L -asparaginase Lubkowski, Jacek; Dauter, Miroslawa; Aghaiypour, Khosrow Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 1 https://doi.org/10.1107/S0907444902019443	journal	December 2002
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity Offman, Marc N.; Krol, Marcin; Patel, Naina Blood, Vol. 117, Issue 5 https://doi.org/10.1182/blood-2010-07-298422	journal	February 2011

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The differential ability of asparagine and glutamine in promoting the closed/active enzyme conformation rationalizes the Wolinella succinogenes L-asparaginase substrate specificity Nguyen, Hien Anh; Durden, Donald L.; Lavie, Arnon Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep41643	journal	January 2017
Design and Characterization of Erwinia Chrysanthemi l-Asparaginase Variants with Diminished l-Glutaminase Activity Nguyen, Hien Anh; Su, Ying; Lavie, Arnon Journal of Biological Chemistry, Vol. 291, Issue 34 https://doi.org/10.1074/jbc.m116.728485	journal	June 2016
Development of L-Asparaginase Biobetters: Current Research Status and Review of the Desirable Quality Profiles Brumano, Larissa Pereira; da Silva, Francisco Vitor Santos; Costa-Silva, Tales Alexandre Frontiers in Bioengineering and Biotechnology, Vol. 6 https://doi.org/10.3389/fbioe.2018.00212	journal	January 2019
Engineering Cell‐Free Protein Synthesis for High‐Yield Production and Human Serum Activity Assessment of Asparaginase: Toward On‐Demand Treatment of Acute Lymphoblastic Leukemia Hunt, J. Porter; Wilding, Kristen M.; Barnett, R. Jordan Biotechnology Journal, Vol. 15, Issue 4 https://doi.org/10.1002/biot.201900294	journal	April 2020
Glutamine Metabolism in Cancer Li, Ting; Le, Anne The Heterogeneity of Cancer Metabolism https://doi.org/10.1007/978-3-319-77736-8_2	book	January 2018
L-Asparaginase from E. chrysanthemi expressed in glycoswitch ^® : effect of His-Tag fusion on the extracellular expression Effer, Brian; Lima, Guilherme Meira; Cabarca, Sindy Preparative Biochemistry and Biotechnology, Vol. 49, Issue 7 https://doi.org/10.1080/10826068.2019.1599396	journal	April 2019
Structure and function of the thermostable L -asparaginase from Thermococcus kodakarensis Guo, Jingxu; Coker, Alun R.; Wood, Steve P. Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 11 https://doi.org/10.1107/s2059798317014711	journal	October 2017

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