DOCSLIB.ORG

Α-Methylacyl-Coa Racemase and Argininosuccinate Lyase

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Α-Methylacyl-Coa Racemase and Argininosuccinate Lyase A460etukansi.fm Page 1 Friday, May 26, 2006 11:40 AM A 460 OULU 2006 A 460 UNIVERSITY OF OULU P.O. Box 7500 FI-90014 UNIVERSITY OF OULU FINLAND ACTA UNIVERSITATIS OULUENSIS ACTA UNIVERSITATIS OULUENSIS ACTA A SERIES EDITORS SCIENTIAE RERUM Prasenjit Bhaumik NATURALIUM Prasenjit Bhaumik Prasenjit ASCIENTIAE RERUM NATURALIUM Professor Mikko Siponen PROTEIN CRYSTALLOGRAPHIC BHUMANIORA STUDIES TO UNDERSTAND Professor Harri Mantila THE REACTION MECHANISM CTECHNICA Professor Juha Kostamovaara OF ENZYMES: DMEDICA α Professor Olli Vuolteenaho -METHYLACYL-CoA RACEMASE AND ESCIENTIAE RERUM SOCIALIUM Senior assistant Timo Latomaa ARGININOSUCCINATE LYASE FSCRIPTA ACADEMICA Communications Officer Elna Stjerna GOECONOMICA Senior Lecturer Seppo Eriksson EDITOR IN CHIEF Professor Olli Vuolteenaho EDITORIAL SECRETARY Publication Editor Kirsti Nurkkala FACULTY OF SCIENCE, DEPARTMENT OF BIOCHEMISTRY, BIOCENTER OULU, ISBN 951-42-8090-3 (Paperback) UNIVERSITY OF OULU ISBN 951-42-8091-1 (PDF) ISSN 0355-3191 (Print) ISSN 1796-220X (Online) ACTA UNIVERSITATIS OULUENSIS A Scientiae Rerum Naturalium 460 PRASENJIT BHAUMIK PROTEIN CRYSTALLOGRAPHIC STUDIES TO UNDERSTAND THE REACTION MECHANISM OF ENZYMES: α-METHYLACYL-COA RACEMASE AND ARGININOSUCCINATE LYASE Academic Dissertation to be presented with the assent of the Faculty of Science, University of Oulu, for public discussion in Kuusamonsali (Auditorium YB210), Linnanmaa, on June 6th, 2006, at 12 noon OULUN YLIOPISTO, OULU 2006 Copyright © 2006 Acta Univ. Oul. A 460, 2006 Supervised by Professor Rik Wierenga Reviewed by Doctor Anette Henriksen Professor Reijo Lahti ISBN 951-42-8090-3 (Paperback) ISBN 951-42-8091-1 (PDF) http://herkules.oulu.fi/isbn9514280911/ ISSN 0355-3191 (Printed ) ISSN 1796-220X (Online) http://herkules.oulu.fi/issn03553191/ Cover design Raimo Ahonen OULU UNIVERSITY PRESS OULU 2006 Bhaumik, Prasenjit, Protein crystallographic studies to understand the reaction mechanism of enzymes: α-methylacyl-CoA racemase and argininosuccinate lyase Faculty of Science, Department of Biochemistry, University of Oulu, P.O.Box 3000, FI-90014 University of Oulu, Finland, Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014 University of Oulu, Finland Acta Univ. Oul. A 460, 2006 Oulu, Finland Abstract Enzymes catalyze chemical changes in biological systems. Therefore, to understand the chemistry of living systems, it is important to understand the enzyme structure and the chemistry of the enzyme's functional groups which are involved in catalysis. In this study, structure and function relationships of two enzymes, (1) α-methylacyl-CoA racemase from Mycobacterium tuberculosis (MCR) and (2) argininosuccinate lyase from Escherichia coli (eASL) have been studied using X-ray crystallography. The main focus of this study has been understanding the structure-function relationship of MCR. The eASL has been crystallized from a highly concentrated sample of purified recombinant α-methylacyl- CoA racemase in which it occurred as a minor impurity. The structure of eASL has been solved using molecular replacement at 2.44 Å resolution. The enzyme is a tetramer, but in this crystal form there is a dimer in the asymmetric unit. Each active site is constructed from loops of three different subunits. One of these catalytic loops, near residue Ser277 and Ser278, has been disordered in the previous structures of active lyases, but is very well ordered in this structure in one of the subunits due to the presence of two phosphate ions in the respective active site cavity. The positions of these phosphate ions indicate a plausible mode of binding of the succinate moiety of the substrate in the competent catalytic complex and therefore this structure has provided new information on the reaction mechanism of this class of enzymes. α-Methylacyl-CoA racemase (Amacr) catalyzes the racemization of α-methyl-branched CoA esters. An Amacr homologue from the eubacteria Mycobacterium tuberculosis, referred to as MCR, was taken as a model protein. MCR was purified, crystallized and the structure of unliganded protein was determined at 1.8 Å resolution using the MIRAS procedure. The structure shows that the enzyme is an interlocked dimer. To understand the reaction mechanism and the mode of substrate binding, several crystallographic binding studies were done using both wild type MCR and mutant H126A MCR crystals. In particular, the structures of the wild type MCR-complexes with (R, S)-ibuprofenoyl-CoA (1.85 Å), (R)-2- methylmyristoyl-CoA (1.6 Å) and (S)-2-methylmyristoyl-CoA (1.7 Å) were important in this respect. These crystal structures show that Asp156 and His126 are the two catalytic residues which are involved in proton donation and abstraction, respectively; when the (S)-enantiomeric substrate is bound in the active site and vice versa when the (R)-enantiomeric substrate is bound. The tight geometry of the active site also shows that His126 and Asp156 are involved in stabilizing the transition state. These crystal structures show that in the active site of MCR, there is one binding pocket for the CoA part and there are two different binding pockets (R-pocket and S-pocket) connected by a hydrophobic methionine rich surface for binding the fatty acyl part of the substrate. After substrate binding, proton abstraction takes place which produces a planar intermediate. Then, donation of a proton to the other side of the planar intermediate changes the configuration at the chiral center. During the stereochemical interconversion of the two enantiomers, the acyl group moves between R-pocket and S-pocket by sliding over the hydrophobic surface connecting these two pockets. Keywords: α-methylacyl-CoA racemase, argininosuccinate lyase, CoA transferase, proton transfer, racemase To Shrii Shrii Anandamurti Acknowledgements This work was carried out in the Department of Biochemistry and Biocenter Oulu at University of Oulu, during years 2001-2006. Financial support was from University of Oulu, Biocenter Oulu graduate school fellowship, and Tauno Tönningin Research Foundation. Firstly, I would like to warmly thank Professor Rik Wierenga for his excellent supervision, constant enthusiasm and support during this study. When I started my PhD research project I did not have any background in protein crystallography. However, he has been very patient to teach me both theoretical and practical aspects of protein crystallography. During the years of my thesis, there have been several ups and downs in my research, but he has always provided me enthusiasm and encouragement to make new discoveries. His patience, unquenchable curiosity and love for the research have been a great inspiration to me, and his continual support and encouragement have enablead me to complete my PhD thesis. I am also grateful to Professor Kalervo Hiltunen for his collaboration in this project, inspiration and helpful attitude during these years. I also wish to express my sincere thanks to Dr. Petri Kursula, who has been a great tutor and helped me a lot at the beginning of this research project. He has been a great inspiration to me during these years. I would like to thank also the other professors and group leaders of our department for creating such excellent research facilities and enjoyable working atmosphere. I would like to express my sincere thanks to Dr. Werner Schmitz and Professor Ernst Conzelmann from Theodor-Boveri-Institut für Biowissenschaften (Biozentrum) der Universität Würzburg, Würzburg, Germany for their collaboration in this project and giving me an opportunity to work in their laboratory. Dr. Schmitz has been very helpful and provided several interesting compounds for crystallographic binding studies. I would like to thank Dr. Päivi Pirilä for her effort to synthesize important ligands for this research project. I wish to thank all my co-authors for their contributions, especially Dr. Kalle Savolainen for his mutagenesis studies and Dr. Ulrich Bergmann for his help in mass spectrometric analysis of proteins. I am grateful to Dr. Anette Henriksen and Professor Reijo Lahti for their valuable comments on the manuscript of the thesis. I also thank the members of my thesis committee, especially Docent Tuomo Glumoff for his constructive criticism and comments which have helped me to carry out the research in the right direction. I would like to thank all the former and present members of RW group for everyday collaboration and many cheerful moments. I would like to specially thank Ville Ratas for his help at the beginning of this project. I wish to thank Dr. Antti Haapalainen for sharing tension and lots of fun during several synchrotron trips. I would like to thank Dr. Inari Kursula, Dr. Anu Mursula, Dr. Kristian Koski, Jukka Taskinen, Mikko Salin, Viivi Majava, Gitte Meriläinen, Markus Alahuhta, Mira Pekkala and Sanna Partanen for their help, company during these years. I wish to extend my sincere thanks to all the staff of our department. I want to thank Virpi Hannus, Anneli Kaattari, Pia Askonen and Tuula Koret for their kind help with many practical tasks. I would like to thank Kyösti Keränen and Jaakko Keskitalo for maintaining the X-ray equipment in proper condition for the datacollection during these years (especially in the summer time!). Jyrki Hänninen, André Juffer, Miki Kallio and Ari-Pekka Kvist are also acknowledged for setting up and maintaining computer systems. I sincerely thank all the people of the “Indian and Asian community” who have given me company and have always helped me during my stay in Oulu. I would like to thank Dr. Mahesh Somani, Satyan Sharma and Sharat Khungar for their friendship. I would like to specially thank my very good friend Dr. Baylie Damtie for his friendship and help. I also wish to express my big and special thanks to my very close and old friends Ranada, Saurabhda and Saurabhda’s wife Gargee for their support and help. It would have been very difficult to complete my dissertation without the help and support of my family members and close relatives. I would like to express my sincere thanks to my father and mother for their love, support and encouragement. I would like to thank my brother Surajit (Sintu) for his support and cheers.
Load more

Recommended publications
  • Dr. Martin St. Maurice's Publications
    Dr. Martin St. Maurice’s Publications 2013 Lin, Y., and St. Maurice, M. 2013. The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family. Biochemistry. 52: 690-700. 2012 Waldrop, G.L., Holden, H.M., and St. Maurice, M. 2012. The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms. Protein Science 21(11):1597-1619. Adina-Zada, A., Sereeruk, C., Jitrapakdee, S., Zeczycki, T.N., St. Maurice, M., Cleland, W.W., Wallace, J.C., and Attwood, P.V. 2012. Roles of Arg427 and Arg472 in the binding and allosteric effects of acetyl CoA in pyruvate carboxylase. Biochemistry 51(41): 1597-1619. 2011 Adina-Zada, A., Hazra, R., Sereeruk, C., Jitrapakdee, S., Zeczycki, T.N., St. Maurice, M., Cleland, W.W., Wallace, J.C., and Attwood, P.V. 2011. Probing the allosteric activation of pyruvate carboxylase using 2′,3′-O-(2,4,6-trinitrophenyl) adenosine 5′-triphosphate as a fluorescent mimic of the allosteric activator acetyl CoA. Arch. Biochem. Biophys. 117-126. Zeczycki, T.N., Menefee, A.L., Jitrapakdee, S., Wallace, J.C., Attwood, P.V., St. Maurice, M. and Cleland, W.W. 2011. Activation and inhibition of pyruvate carboxylase from Rhizobium etli. Biochemistry. 9694-9707. Lietzan, A.D., Menefee, A.L., Zeczycki, T.N., Kumar, S., Attwood, P.V., Wallace, J.C., Cleland, W.W. and St. Maurice, M. 2011. Interaction between the biotin carrier domain and the biotin carboxylase domain in the structure of Rhizobium etli pyruvate carboxylase. Biochemistry. 9708-9723. Zeczycki, T.N., Menefee, A.L., Adina-Zada, A., Surinya, K.H., Wallace, J.C., Attwood, P.V., St.
    [Show full text]
  • Fulltext01.Pdf
    http://www.diva-portal.org This is the published version of a paper published in Cellular and Molecular Life Sciences (CMLS). Citation for the original published paper (version of record): Cava, F., Lam, H., de Pedro, M., Waldor, M. (2011) Emerging knowledge of regulatory roles of D-amino acids in bacteria. Cellular and Molecular Life Sciences (CMLS), 68(5): 817-831 http://dx.doi.org/10.1007/s00018-010-0571-8 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-81861 Cell. Mol. Life Sci. (2011) 68:817–831 DOI 10.1007/s00018-010-0571-8 Cellular and Molecular Life Sciences REVIEW Emerging knowledge of regulatory roles of D-amino acids in bacteria Felipe Cava • Hubert Lam • Miguel A. de Pedro • Matthew K. Waldor Received: 13 July 2010 / Revised: 24 September 2010 / Accepted: 14 October 2010 / Published online: 14 December 2010 Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract The D-enantiomers of amino acids have been Keywords D-amino acid Á Racemase Á Stationary phase Á thought to have relatively minor functions in biological Peptidoglycan Á Biofilm Á Regulation processes. While L-amino acids clearly predominate in nat- ure, D-amino acids are sometimes found in proteins that are Abbreviations not synthesized by ribosomes, and D-Ala and D-Glu are NRP Nonribosomal peptide routinely found in the peptidoglycan cell wall of bacteria. PG Peptidoglycan Here, we review recent findings showing that D-amino acids GlcNAc N-acetyl glucosamine have previously unappreciated regulatory roles in the bac- MurNAc N-acetylmuramic acid terial kingdom.
    [Show full text]
  • Coordinated Slowing of Metabolism in Enteric Bacteria Under Nitrogen
    Coordinated Slowing of Metabolism in Enteric Bacteria under Nitrogen Limitation: A Perspective Ned S. Wingreen NEC Research Institute, 4 Independence Way Princeton, New Jersey 08540 and Department of Physics, University of California Berkeley, CA 94720 Sydney Kustu Department of Plant Biology, Molecular and Cell Biology University of California, Berkeley, CA 94720 Abstract It is natural to ask how bacteria coordinate metabolism when depletion of an essential nutrient limits their growth, and they must slow their entire rate of biosyn- thesis. A major nutrient with a fluctuating abundance is nitrogen. The growth rate of enteric bacteria under nitrogen-limiting conditions is known to correlate with the internal concentration of free glutamine, the glutamine pool. Here we compare the patterns of utilization of L-glutamine and L-glutamate, the two central inter- mediates of nitrogen metabolism. Monomeric precursors of all of the cell’s macro- molecules – proteins, nucleic acids, and surface polymers – require the amide group of glutamine at the first dedicated step of biosynthesis. This is the case even though only a minority (∼12%) of total cell nitrogen derives from glutamine. In contrast, the amino group of glutamate, which provides the remainder of cell nitrogen, is arXiv:physics/0110037v1 [physics.bio-ph] 12 Oct 2001 generally required late in biosynthetic pathways, e.g. in transaminase reactions for amino acid synthesis. We propose that the pattern of glutamine dependence coor- dinates the decrease in biosynthesis under conditions of nitrogen limitation. Hence, the glutamine pool plays a global regulatory role in the cell. 1 INTRODUCTION Enteric bacteria are notable for their varying environment.
    [Show full text]
  • Title Non-Stereospecific Transamination Catalyzed by Pyridoxal Phosphate-Dependent Amino Acid Racemases of Broad Substrate Speci
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Non-stereospecific Transamination Catalyzed by Pyridoxal Phosphate-dependent Amino Acid Racemases of Broad Title Substrate Specificity (MOLECULAR BIOFUNCTION- Molecular Microbial Science) Esaki, Nobuyoshi; Yoshimura, Tohru; Soda, Kenji; Lim, Author(s) Young Hee Citation ICR annual report (1999), 5: 46-47 Issue Date 1999-03 URL http://hdl.handle.net/2433/65185 Right Type Article Textversion publisher Kyoto University 46 ICR Annual Report, Vol. 5, 1998 Non-stereospecific Transamination Catalyzed by Pyridoxal Phosphate-dependent Amino Acid Racemases of Broad Substrate Specificity Nobuyoshi Esaki, Tohru Yoshimura, Kenji Soda and Young Hee Lim Pyridoxal 5’-phosphate-dependent amino acid racemases of broad substrate specificity catalyze transamination as a side-reaction. We studied the stereospecificities for hydrogen abstraction from C-4’ of the bound pyridoxamine 5’-phosphate during transamination from pyridoxamine 5’-phosphate to pyruvate catalyzed by three amino acid racemases of broad substrate specificity. When the enzymes were incubated with (4’S)- or (4’R)-[4’-3H]- pyridoxamine 5’-phosphate in the presence of pyruvate, tritium was released into the solvent from both pyridoxamine 5’-phosphates. Thus, these enzymes abstract a hydrogen non-stereospecifically from C-4’ of the coenzyme in contrast to the other pyridoxal 5’-phosphate-dependent enzymes so far studied which catalyze the stereospecific hydrogen removal. Amino acid racemase of broad substrate specificity from Pseudomonas putida produced D- and L-glutamate from α-ketoglutarate through the transamination with L-ornithine. Because glutamate does not serve as a substrate for racemization, the enzyme catalyzed the non-stereospecific overall transamination between L-ornithine and α-ketoglutarate.
    [Show full text]
  • Letters to Nature
    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
    [Show full text]
  • Exploring the Chemistry and Evolution of the Isomerases
    Exploring the chemistry and evolution of the isomerases Sergio Martínez Cuestaa, Syed Asad Rahmana, and Janet M. Thorntona,1 aEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Edited by Gregory A. Petsko, Weill Cornell Medical College, New York, NY, and approved January 12, 2016 (received for review May 14, 2015) Isomerization reactions are fundamental in biology, and isomers identifier serves as a bridge between biochemical data and ge- usually differ in their biological role and pharmacological effects. nomic sequences allowing the assignment of enzymatic activity to In this study, we have cataloged the isomerization reactions known genes and proteins in the functional annotation of genomes. to occur in biology using a combination of manual and computa- Isomerases represent one of the six EC classes and are subdivided tional approaches. This method provides a robust basis for compar- into six subclasses, 17 sub-subclasses, and 245 EC numbers cor- A ison and clustering of the reactions into classes. Comparing our responding to around 300 biochemical reactions (Fig. 1 ). results with the Enzyme Commission (EC) classification, the standard Although the catalytic mechanisms of isomerases have already approach to represent enzyme function on the basis of the overall been partially investigated (3, 12, 13), with the flood of new data, an integrated overview of the chemistry of isomerization in bi- chemistry of the catalyzed reaction, expands our understanding of ology is timely. This study combines manual examination of the the biochemistry of isomerization. The grouping of reactions in- chemistry and structures of isomerases with recent developments volving stereoisomerism is straightforward with two distinct types cis-trans in the automatic search and comparison of reactions.
    [Show full text]
  • Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts
    Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts Jinzhi He1, Qichao Tu2,3, Yichen Ge1, Yujia Qin3, Bomiao Cui1, Xiaoyu Hu1, Yuxia Wang1, Ye Deng4, Kun Wang1, Joy D. Van Nostrand3, Jiyao Li 1, Jizhong Zhou3,5,6, Yan Li 1, Xuedong Zhou1 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China 2 Department of Marine Sciences, Ocean College, Zhejiang University, Hangzhou, China 3 Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, USA 4 Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China 5 State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China 6 Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, USA Abstract Caries is one of the most prevalent and costly infectious diseases affecting humans of all ages. It is initiated by cariogenic supragingival dental plaques forming on salivacoated tooth surfaces, yet the etiology remains elusive. To determine which microbial populations may predispose a patient to caries, we report here an in-depth and comprehensive view of the microbial community associated with supragingival dental plaque collected from the healthy teeth of caries patients and healthy adults. We found that microbial communities from caries patients had a higher evenness and inter-individual variations but simpler ecological networks compared to healthy controls despite the overall taxonomic structure being similar. Genera including Selenomonas, Treponema, Atopobium, and Bergeriella were distributed differently between the caries and healthy groups with disturbed co- occurrence patterns.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000702945Cyc: Clostridium sp. KNHs205 Cellular Overview Connections between pathways are omitted for legibility.
    [Show full text]
  • Is D-Aspartate Produced by Glutamic-Oxaloacetic Transaminase-1 Like 1 (Got1l1): a Putative Aspartate Racemase?
    Amino Acids (2015) 47:79–86 DOI 10.1007/s00726-014-1847-3 ORIGINAL ARTICLE Is d-aspartate produced by glutamic-oxaloacetic transaminase-1 like 1 (Got1l1): a putative aspartate racemase? Ayumi Tanaka-Hayashi · Shuuhei Hayashi · Ran Inoue · Tomokazu Ito · Kohtarou Konno · Tomoyuki Yoshida · Masahiko Watanabe · Tohru Yoshimura · Hisashi Mori Received: 23 July 2014 / Accepted: 25 September 2014 / Published online: 7 October 2014 © The Author(s) 2014. This article is published with open access at Springerlink.com Abstract D-Aspartate is an endogenous free amino acid hippocampus. The recombinant Got1l1 expressed in mam- in the brain, endocrine tissues, and exocrine tissues in malian cells showed L-aspartate aminotransferase activity, mammals, and it plays several physiological roles. In the but lacked aspartate racemase activity. These findings sug- testis, D-aspartate is detected in elongate spermatids, Ley- gest that Got1l1 is not the major aspartate racemase and dig cells, and Sertoli cells, and implicated in the synthesis there might be an as yet unknown D-aspartate-synthesizing and release of testosterone. In the hippocampus, D-aspartate enzyme. strongly enhances N-methyl-D-aspartate receptor-depend- ent long-term potentiation and is involved in learning and Keywords Glutamic-oxaloacetic transaminase-1 like 1 · memory. The existence of aspartate racemase, a candidate D-Aspartate · Knockout mice · Testis · Hippocampus · enzyme for D-aspartate production, has been suggested. Recombinant protein expression Recently, mouse glutamic-oxaloacetic transaminase 1-like 1 (Got1l1) has been reported to synthesize substantially Abbreviations D-aspartate from L-aspartate and to be involved in adult Got1l1 Glutamic-oxaloacetic transaminase-1 like 1 neurogenesis.
    [Show full text]
  • Peroxisomes in Brain Development and Function☆
    BBAMCR-17753; No. of pages: 22; 4C: 3, 5, 10 Biochimica et Biophysica Acta xxx (2015) xxx–xxx Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamcr Peroxisomes in brain development and function☆ Johannes Berger ⁎, Fabian Dorninger, Sonja Forss-Petter, Markus Kunze Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria article info abstract Article history: Peroxisomes contain numerous enzymatic activities that are important for mammalian physiology. Patients lacking Received 15 October 2015 either all peroxisomal functions or a single enzyme or transporter function typically develop severe neurological def- Received in revised form 4 December 2015 icits, which originate from aberrant development of the brain, demyelination and loss of axonal integrity, neuroin- Accepted 9 December 2015 flammation or other neurodegenerative processes. Whilst correlating peroxisomal properties with a compilation of Available online xxxx pathologies observed in human patients and mouse models lacking all or individual peroxisomal functions, we dis- fi Keywords: cuss the importance of peroxisomal metabolites and tissue- and cell type-speci c contributions to the observed Lipid metabolism brain pathologies. This enables us to deconstruct the local and systemic contribution of individual metabolic path- Plasmalogen ways to specific brain functions. We also review the recently discovered variability of pathological symptoms in Zellweger spectrum disorder cases with unexpectedly mild presentation of peroxisome biogenesis disorders. Finally, we explore the emerging ev- D-bifunctional protein deficiency idence linking peroxisomes to more common neurological disorders such as Alzheimer's disease, autism and amyo- X-linked adrenoleukodystrophy trophic lateral sclerosis.
    [Show full text]
  • (NMDA) Receptor Coactivation: Inhibition of D-Serine Synthesis by Converting Serine Racemase Into an Eliminase
    A new strategy to decrease N-methyl-D-aspartate (NMDA) receptor coactivation: Inhibition of D-serine synthesis by converting serine racemase into an eliminase Roge´ rio Panizzutti*, Joari De Miranda*, Ca´ tia S. Ribeiro*, Simone Engelender†, and Herman Wolosker*‡ *Departamento de Bioquimica Medica, Instituto de Ciencias Biomedicas, and †Center for Neurodegenerative Diseases, Departamento de Anatomia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21491-590, Brazil Edited by Solomon H. Snyder, Johns Hopkins University School of Medicine, Baltimore, MD, and approved February 23, 2001 (received for review January 3, 2001) Serine racemase is a brain-enriched enzyme that synthesizes D- serine racemase genes (9, 10). The distribution of serine race- serine, an endogenous modulator of the glycine site of N-methyl- mase was closely similar to that of endogenous D-serine with the D-aspartate (NMDA) receptors. We now report that serine race- highest concentrations in the forebrain and negligible levels in mase catalyzes an elimination reaction toward a nonphysiological the brainstem. Both D-serine and serine racemase occur in substrate that provides a powerful tool to study its neurobiological astrocytes, in regions enriched in NMDA receptors, suggesting role and will be useful to develop selective enzyme inhibitors. that serine racemase physiologically synthesizes D-serine to Serine racemase catalyzes robust elimination of L-serine O-sulfate regulate NMDA receptor activity (9). that is 500 times faster than the physiological racemization reac- As an endogenous coagonist of NMDA receptors, D-serine tion, generating sulfate, ammonia, and pyruvate. This reaction may play a role in several pathological conditions related to provides the most simple and sensitive assay to detect the enzyme NMDA receptor dysfunction.
    [Show full text]
  • Discovery of a Novel Amino Acid Racemase Through Exploration of Natural Variation in Arabidopsis Thaliana
    Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana Renee C. Straucha,b, Elisabeth Svedinc, Brian Dilkesc, Clint Chappled, and Xu Lia,b,1 aPlants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081; bDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695; cDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907; and dDepartment of Biochemistry, Purdue University, West Lafayette, IN 47907 Edited by Justin O. Borevitz, Australian National University, Canberra, ACT, Australia, and accepted by the Editorial Board August 1, 2015 (received for review February 16, 2015) Plants produce diverse low-molecular-weight compounds via spe- contribution to the variation in at least three-fourths of detected cialized metabolism. Discovery of the pathways underlying produc- mass peaks (8). tion of these metabolites is an important challenge for harnessing Here we describe an integrated transdisciplinary platform, the huge chemical diversity and catalytic potential in the plant king- combining metabolomics, genetics, and genomics, to exploit the dom for human uses, but this effort is often encumbered by the biochemical and genetic diversity of natural accessions of the necessity to initially identify compounds of interest or purify a cata- model plant A. thaliana to uncover associations between genes lyst involved in their synthesis. As an alternative approach, we have and metabolites. Using this platform, we linked a differentially performed untargeted metabolite profiling and genome-wide asso- accumulating metabolite, identified through chemical analysis as ciation analysis on 440 natural accessions of Arabidopsis thaliana. N-malonyl-D-allo-isoleucine (NMD-Ile), to a previously unchar- This approach allowed us to establish genetic linkages between acterized gene identified as an amino acid racemase through metabolites and genes.
    [Show full text]