1
|
Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H. Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima. FEBS J 2018; 286:601-614. [PMID: 30548096 DOI: 10.1111/febs.14720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/29/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022]
Abstract
Various d-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional d-alanine (d-Ala) and d-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both l-lysine (l-Lys) and d-Lys, but not meso-diaminopimelate (meso-Dpm). d-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterized a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the d-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward d- and l-Lys, and also had relatively high activity toward d- and l-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerization activity toward ll- and meso-Dpm, and also measurably racemized certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of d-Lys and d-Ala for use as peptidoglycan components, and that Dpm epimerase converts ll-Dpm to meso-Dpm, a precursor in the l-Lys biosynthetic pathway.
Collapse
Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| |
Collapse
|
2
|
Rossignoli G, Grottesi A, Bisello G, Montioli R, Borri Voltattorni C, Paiardini A, Bertoldi M. Cysteine 180 Is a Redox Sensor Modulating the Activity of Human Pyridoxal 5'-Phosphate Histidine Decarboxylase. Biochemistry 2018; 57:6336-6348. [PMID: 30346159 DOI: 10.1021/acs.biochem.8b00625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histidine decarboxylase is a pyridoxal 5'-phosphate enzyme catalyzing the conversion of histidine to histamine, a bioactive molecule exerting its role in many modulatory processes. The human enzyme is involved in many physiological functions, such as neurotransmission, gastrointestinal track function, cell growth, and differentiation. Here, we studied the functional properties of the human enzyme and, in particular, the effects exerted at the protein level by two cysteine residues: Cys-180 and Cys-418. Surprisingly, the enzyme exists in an equilibrium between a reduced and an oxidized form whose extent depends on the redox state of Cys-180. Moreover, we determined that (i) the two enzymatic redox species exhibit modest structural changes in the coenzyme microenvironment and (ii) the oxidized form is slightly more active and stable than the reduced one. These data are consistent with the model proposed by bioinformatics analyses and molecular dynamics simulations in which the Cys-180 redox state could be responsible for a structural transition affecting the C-terminal domain reorientation leading to active site alterations. Furthermore, the biochemical properties of the purified C180S and C418S variants reveal that C180S behaves like the reduced form of the wild-type enzyme, while C418S is sensitive to reductants like the wild-type enzyme, thus allowing the identification of Cys-180 as the redox sensitive switch. On the other hand, Cys-418 appears to be a residue involved in aggregation propensity. A possible role for Cys-180 as a regulatory switch in response to different cellular redox conditions could be suggested.
Collapse
Affiliation(s)
- Giada Rossignoli
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | | | - Giovanni Bisello
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | - Carla Borri Voltattorni
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli" , University "La Sapienza", Rome , P.zale A. Moro 5 , 00185 Roma , Italy
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement , University of Verona , Strada Le Grazie, 8 , 37134 Verona , Italy
| |
Collapse
|
3
|
Adachi M, Shimizu R, Kato S, Oikawa T. The first identification and characterization of a histidine-specific amino acid racemase, histidine racemase from a lactic acid bacterium, Leuconostoc mesenteroides subsp. sake NBRC 102480. Amino Acids 2018; 51:331-343. [PMID: 30377839 DOI: 10.1007/s00726-018-2671-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/19/2018] [Indexed: 12/22/2022]
Abstract
We expressed a histidine racemase from Leuconostoc mesenteroides subsp. sake NBRC 102480 (Lm-HisR) successively in a soluble fraction of Escherichia coli BL21 (DE3) and then highly purified it from the cell-free extract. Lm-HisR showed amino acid racemase activity on histidine specifically. This is the first example of an amino acid racemase specifically acting on histidine. Phylogenetic analysis of Lm-HisR showed that Lm-HisR was located far from the cluster of alanine racemases reported thus far and only in lactic acid bacteria of the genus Leuconostoc. Alignment of the primary structure of Lm-HisR with those of lysine and alanine racemases and alanine racemase homologs previously reported revealed that the PLP-binding lysine and catalytic tyrosine were completely conserved, and some residues that are unique to the phylogenetic branch of Lm-HisR, Phe44, Ser45, Thr174, Thr206, His286, Ser287, Phe292, Gly312, Val357, and Ala358 were identified. We determined the crystal structure of Lm-HisR complexed with PLP at a 2.1-Å resolution. The crystal structure contained four molecules (two dimers) in the asymmetric unit. When comparing the 3D structure of Lm-HisR with those of racemases from Geobacillus stearothermophilus and Oenococcus oeni, Met315 was completely conserved, but Val357 was not. In addition, two significant differences were observed between Lm-HisR and G. stearothermophilus alanine racemase. Phe44 and His286 in Lm-HisR corresponded to Tyr43 and Tyr284 in G. stearothermophilus alanine racemase, respectively. Based on the structural analysis, comparison with alanine racemase, and docking simulation, three significant residues, Phe44, His286, and Val357, were identified that may control the substrate specificity of Lm-HisR.
Collapse
Affiliation(s)
- Motoyasu Adachi
- Tokai Quantum Beam Science Center, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Rumi Shimizu
- Tokai Quantum Beam Science Center, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Shiro Kato
- Kansai University High Technology Research Center, 3-3-35 Yamate-Cho, Suita, Osaka, 564-8680, Japan
- International Institute of Rare Sugar Research and Education, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan
| | - Tadao Oikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka, 564-8680, Japan.
- Kansai University High Technology Research Center, 3-3-35 Yamate-Cho, Suita, Osaka, 564-8680, Japan.
| |
Collapse
|
4
|
Hernández SB, Cava F. Environmental roles of microbial amino acid racemases. Environ Microbiol 2015; 18:1673-85. [DOI: 10.1111/1462-2920.13072] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/15/2015] [Accepted: 09/27/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Sara B. Hernández
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
| |
Collapse
|
5
|
Espaillat A, Carrasco-López C, Bernardo-García N, Pietrosemoli N, Otero LH, Álvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F. Structural basis for the broad specificity of a new family of amino-acid racemases. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:79-90. [PMID: 24419381 PMCID: PMC4984259 DOI: 10.1107/s1399004713024838] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/05/2013] [Indexed: 02/02/2023]
Abstract
Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family members.
Collapse
Affiliation(s)
- Akbar Espaillat
- Centro de Biología Molecular ‘Severo Ochoa’, Universidad Autónoma de Madrid–Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’–CSIC, 28006 Madrid, Spain
| | - Noelia Bernardo-García
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’–CSIC, 28006 Madrid, Spain
| | | | - Lisandro H. Otero
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’–CSIC, 28006 Madrid, Spain
| | - Laura Álvarez
- Centro de Biología Molecular ‘Severo Ochoa’, Universidad Autónoma de Madrid–Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Miguel A. de Pedro
- Centro de Biología Molecular ‘Severo Ochoa’, Universidad Autónoma de Madrid–Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | | | - Brigid M. Davis
- Division of Infectious Diseases, Brigham and Women’s Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’–CSIC, 28006 Madrid, Spain
| | - Felipe Cava
- Centro de Biología Molecular ‘Severo Ochoa’, Universidad Autónoma de Madrid–Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| |
Collapse
|
6
|
Conti P, Tamborini L, Pinto A, Blondel A, Minoprio P, Mozzarelli A, De Micheli C. Drug Discovery Targeting Amino Acid Racemases. Chem Rev 2011; 111:6919-46. [DOI: 10.1021/cr2000702] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Conti
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS-URA 2185, Département de Biologie Structurale et Chimie, 25 rue du Dr. Roux, 75724 Paris, France
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosoma; Département d’Infection et Epidémiologie; 25 rue du Dr. Roux, 75724 Paris, France
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, via G. P. Usberti 23/A, 43100 Parma, Italy
- Istituto di Biostrutture e Biosistemi, viale Medaglie d’oro, Roma, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| |
Collapse
|