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Telek A, Molnár Z, Takács K, Varga B, Grolmusz V, Tasnádi G, Vértessy BG. Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining. Appl Microbiol Biotechnol 2024; 108:101. [PMID: 38229296 DOI: 10.1007/s00253-023-12871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.
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Grants
- K119493 National Research, Development and Innovation Office
- K135231 National Research, Development and Innovation Office
- VEKOP-2.3.2-16-2017-00013 National Research, Development and Innovation Office
- NKP-2018-1.2.1-NKP-2018-00005 National Research, Development and Innovation Office
- TKP2021-EGA-02 National Research, Development and Innovation Office
- ÚNKP-22-4-II-BME-158 National Research, Development and Innovation Office
- RRF-2.3.1-21-2022-000 15 National Research, Development and Innovation Office
- C1580174 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- ELTE TKP 2021-NKTA-62 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- 2022-1.2.2-TÉT-IPARI-UZ-2022-00003 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
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Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary.
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2
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Kaličanin N, Balaž AM, Prodanović O, Prodanović R. Heterologous Expression and Partial Characterization of a Putative Opine Dehydrogenase from a Metagenomic Sequence of Desulfohalobium retbaense. Chembiochem 2023; 24:e202300414. [PMID: 37531452 DOI: 10.1002/cbic.202300414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/13/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023]
Abstract
The aim of this research was to prove the function of the putative opine dehydrogenase from Desulfohalobium retbaense and to characterize the enzyme in terms of functional and kinetic parameters. A putative opine dehydrogenase was identified from a metagenomic library by a sequence-based technique search of the metagenomic library, and afterward was successfully heterologously produced in Escherichia coli. In order to examine its potential for applications in the synthesis of secondary amines, first the substrate specificity of the enzyme towards different amino donors and amino acceptors was determined. The highest affinity was observed towards small amino acids, preferentially L-alanine, and when it comes to α-keto acids, pyruvate proved to be a preferential amino acceptor. The highest activity was observed at pH 6.5 in the absence of salts. The enzyme showed remarkable stability in a wide range of experimental conditions, such as broad pH stability (from 6.0-11.0 after 30 min incubation in buffers at a certain pH), stability in the presence of NaCl up to 3.0 M for 24 h, it retained 80 % of the initial activity after 1 h incubation at 45 °C, and 65 % of the initial activity after 24 h incubation in 30 % dimethyl sulfoxide.
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Affiliation(s)
- Nevena Kaličanin
- University of Belgrade-Institute of Chemistry Technology and Metallurgy National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
| | - Ana Marija Balaž
- University of Belgrade-Institute of Chemistry Technology and Metallurgy National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
- Department of Otorhinolaryngology Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Marchioninistr. 15, 81377, Munich, Germany
| | - Olivera Prodanović
- University of Belgrade-Institute for Multidisciplinary Research, Kneza Višeslava 1, 11030, Belgrade, Serbia
| | - Radivoje Prodanović
- Department of Biochemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
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3
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Telek A, Molnár Z, Vértessy BG, Tasnádi G. Opine dehydrogenases, an underexplored enzyme family for the enzymatic synthesis of chiral amines. Biotechnol Bioeng 2023; 120:2793-2808. [PMID: 37334502 DOI: 10.1002/bit.28469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/17/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023]
Abstract
Opines and opine-type chemicals are valuable natural products with diverse biochemical roles, and potential synthetic building blocks of bioactive compounds. Their synthesis involves reductive amination of ketoacids with amino acids. This transformation has high synthetic potential in producing enantiopure secondary amines. Nature has evolved opine dehydrogenases for this chemistry. To date, only one enzyme has been used as biocatalyst, however, analysis of the available sequence space suggests more enzymes to be exploited in synthetic organic chemistry. This review summarizes the current knowledge of this underexplored enzyme class, highlights key molecular, structural, and catalytic features with the aim to provide a comprehensive general description of opine dehydrogenases, thereby supporting future enzyme discovery and protein engineering studies.
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Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
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4
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McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL. Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores. J Biol Chem 2019; 294:17988-18001. [PMID: 31615895 DOI: 10.1074/jbc.ra119.011059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/10/2019] [Indexed: 11/06/2022] Open
Abstract
Pseudopaline and staphylopine are opine metallophores biosynthesized by Pseudomonas aeruginosa and Staphylococcus aureus, respectively. The final step in opine metallophore biosynthesis is the condensation of the product of a nicotianamine (NA) synthase reaction (i.e. l-HisNA for pseudopaline and d-HisNA for staphylopine) with an α-keto acid (α-ketoglutarate for pseudopaline and pyruvate for staphylopine), which is performed by an opine dehydrogenase. We hypothesized that the opine dehydrogenase reaction would be reversible only for the opine metallophore product with (R)-stereochemistry at carbon C2 of the α-keto acid (prochiral prior to catalysis). A kinetic analysis using stopped-flow spectrometry with (R)- or (S)-staphylopine and kinetic and structural analysis with (R)- and (S)-pseudopaline confirmed catalysis in the reverse direction for only (R)-staphylopine and (R)-pseudopaline, verifying the stereochemistry of these two opine metallophores. Structural analysis at 1.57-1.85 Å resolution captured the hydrolysis of (R)-pseudopaline and allowed identification of a binding pocket for the l-histidine moiety of pseudopaline formed through a repositioning of Phe-340 and Tyr-289 during the catalytic cycle. Transient-state kinetic analysis revealed an ordered release of NADP+ followed by staphylopine, with staphylopine release being the rate-limiting step in catalysis. Knowledge of the stereochemistry for opine metallophores has implications for future studies involving kinetic analysis, as well as opine metallophore transport, metal coordination, and the generation of chiral amines for pharmaceutical development.
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Affiliation(s)
- Jeffrey S McFarlane
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Jian Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Sanshan Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University, Chicago, Illinois 60660
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
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5
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Hajjar C, Fanelli R, Laffont C, Brutesco C, Cullia G, Tribout M, Nurizzo D, Borezée-Durant E, Voulhoux R, Pignol D, Lavergne J, Cavelier F, Arnoux P. Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis. J Am Chem Soc 2019; 141:5555-5562. [DOI: 10.1021/jacs.9b01676] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christine Hajjar
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
| | - Roberto Fanelli
- Institut des Biomolécules Max Mousseron, IBMM, UMR-5247, CNRS, Université Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Clémentine Laffont
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
| | - Catherine Brutesco
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
| | - Gregorio Cullia
- Institut des Biomolécules Max Mousseron, IBMM, UMR-5247, CNRS, Université Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Mathilde Tribout
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Elise Borezée-Durant
- Micalis Institute, INRA, AgroParisTech, University Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Romé Voulhoux
- Institut de Microbiologie de la Méditerranée, CNRS LCB UMR 7283, Aix Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - David Pignol
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
| | - Jérôme Lavergne
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
| | - Florine Cavelier
- Institut des Biomolécules Max Mousseron, IBMM, UMR-5247, CNRS, Université Montpellier, ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pascal Arnoux
- Aix Marseille Université, CEA, CNRS,
BIAM, F-13108 Saint Paul-Lez-Durance, France
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6
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Tseliou V, Masman MF, Böhmer W, Knaus T, Mutti FG. Mechanistic Insight into the Catalytic Promiscuity of Amine Dehydrogenases: Asymmetric Synthesis of Secondary and Primary Amines. Chembiochem 2019; 20:800-812. [PMID: 30489013 PMCID: PMC6472184 DOI: 10.1002/cbic.201800626] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 12/18/2022]
Abstract
Biocatalytic asymmetric amination of ketones, by using amine dehydrogenases (AmDHs) or transaminases, is an efficient method for the synthesis of α-chiral primary amines. A major challenge is to extend amination to the synthesis of secondary and tertiary amines. Herein, for the first time, it is shown that AmDHs are capable of accepting other amine donors, thus giving access to enantioenriched secondary amines with conversions up to 43 %. Surprisingly, in several cases, the promiscuous formation of enantiopure primary amines, along with the expected secondary amines, was observed. By conducting practical laboratory experiments and computational experiments, it is proposed that the promiscuous formation of primary amines along with secondary amines is due to an unprecedented nicotinamide (NAD)-dependent formal transamination catalysed by AmDHs. In nature, this type of mechanism is commonly performed by pyridoxal 5'-phosphate aminotransferase and not by dehydrogenases. Finally, a catalytic pathway that rationalises the promiscuous NAD-dependent formal transamination activity and explains the formation of the observed mixture of products is proposed. This work increases the understanding of the catalytic mechanism of NAD-dependent aminating enzymes, such as AmDHs, and will aid further research into the rational engineering of oxidoreductases for the synthesis of α-chiral secondary and tertiary amines.
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Affiliation(s)
- Vasilis Tseliou
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Marcelo F. Masman
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Wesley Böhmer
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tanja Knaus
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Francesco G. Mutti
- van 't Hoff Institute for Molecular SciencesHIMS-BiocatUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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7
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Asano Y. Screening and development of enzymes for determination and transformation of amino acids. Biosci Biotechnol Biochem 2019; 83:1402-1416. [PMID: 30621552 DOI: 10.1080/09168451.2018.1559027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.
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Affiliation(s)
- Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Toyama , Japan
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8
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McFarlane JS, Davis CL, Lamb AL. Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J Biol Chem 2018; 293:8009-8019. [PMID: 29618515 PMCID: PMC5971449 DOI: 10.1074/jbc.ra118.002007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/03/2018] [Indexed: 11/06/2022] Open
Abstract
Opine dehydrogenases (ODHs) from the bacterial pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis perform the final enzymatic step in the biosynthesis of a new class of opine metallophores, which includes staphylopine, pseudopaline, and yersinopine, respectively. Growing evidence indicates an important role for this pathway in metal acquisition and virulence, including in lung and burn-wound infections (P. aeruginosa) and in blood and heart infections (S. aureus). Here, we present kinetic and structural characterizations of these three opine dehydrogenases. A steady-state kinetic analysis revealed that the three enzymes differ in α-keto acid and NAD(P)H substrate specificity and nicotianamine-like substrate stereoselectivity. The structural basis for these differences was determined from five ODH X-ray crystal structures, ranging in resolution from 1.9 to 2.5 Å, with or without NADP+ bound. Variation in hydrogen bonding with NADPH suggested an explanation for the differential recognition of this substrate by these three enzymes. Our analysis further revealed candidate residues in the active sites required for binding of the α-keto acid and nicotianamine-like substrates and for catalysis. This work reports the first structural kinetic analyses of enzymes involved in opine metallophore biosynthesis in three important bacterial pathogens of humans.
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Affiliation(s)
- Jeffrey S McFarlane
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Cara L Davis
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045; Department of Chemistry, University of Kansas, Lawrence, Kansas 66045.
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9
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Sharma M, Mangas‐Sanchez J, Turner NJ, Grogan G. NAD(P)H-Dependent Dehydrogenases for the Asymmetric Reductive Amination of Ketones: Structure, Mechanism, Evolution and Application. Adv Synth Catal 2017; 359:2011-2025. [PMID: 30008635 PMCID: PMC6033044 DOI: 10.1002/adsc.201700356] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/11/2017] [Indexed: 11/16/2022]
Abstract
Asymmetric reductive aminations are some of the most important reactions in the preparation of active pharmaceuticals, as chiral amines feature in many of the world's most important drugs. Although many enzymes have been applied to the synthesis of chiral amines, the development of reductive amination reactions that use enzymes is attractive, as it would permit the one-step transformation of readily available prochiral ketones into chiral amines of high optical purity. However, as most natural "reductive aminase" activities operate on keto acids, and many are able to use only ammonia as the amine donor, there is considerable scope for the engineering of natural enzymes for the reductive amination of ketones, and also for the preparation of secondary amines using alkylamines as donors. This review summarises research into the development of NAD(P)H-dependent dehydrogenases for the reductive amination of ketones, including amino acid dehydrogenases (AADHs), natural amine dehydrogenases (AmDHs), opine dehydrogenases (OpDHs) and imine reductases (IREDs). In each case knowledge of the structure and mechanism of the enzyme class is addressed, with a further description of the engineering of those enzymes for the reductive amination of ketones towards primary and also secondary amine products.
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Affiliation(s)
- Mahima Sharma
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkYO10 5DDYorkU.K.
| | - Juan Mangas‐Sanchez
- School of ChemistryUniversity of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK.
| | - Nicholas J. Turner
- School of ChemistryUniversity of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK.
| | - Gideon Grogan
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkYO10 5DDYorkU.K.
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10
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11
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Gohlke H, Hergert U, Meyer T, Mulnaes D, Grieshaber MK, Smits SHJ, Schmitt L. Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion. J Chem Inf Model 2013; 53:2493-8. [PMID: 24066861 DOI: 10.1021/ci400370y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Opine dehydrogenases catalyze the reductive condensation of pyruvate with L-amino acids. Biochemical characterization of alanopine dehydrogenase from Arenicola marina revealed that this enzyme is highly specific for L-alanine. Unbiased molecular dynamics simulations with a homology model of alanopine dehydrogenase captured the binding of L-alanine diffusing from solvent to a putative binding region near a distinct helix-kink-helix motif. These results and sequence comparisons reveal how mutations and insertions within this motif dictate the L-amino acid specificity.
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Affiliation(s)
- Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry and ‡Institute of Biochemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University , 40204 Düsseldorf, Germany
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12
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Miyanaga A, Fujisawa S, Furukawa N, Arai K, Nakajima M, Taguchi H. The crystal structure of d-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase. Biochem Biophys Res Commun 2013; 439:109-14. [DOI: 10.1016/j.bbrc.2013.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 11/26/2022]
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13
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Mondal S, Nagao C, Mizuguchi K. Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores. Protein Eng Des Sel 2010; 23:859-69. [PMID: 20876192 DOI: 10.1093/protein/gzq062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Ketopatoate reductase (KPR) is the second enzyme in the pantothenate (vitamin B(5)) biosynthesis pathway, an essential metabolic pathway identified as a potential target for new antimicrobials. The sequence similarity among putative KPRs is limited and KPR itself belongs to a large superfamily of 6-phosphogluconate dehydrogenases. Therefore, it is necessary to discriminate between true and other enzymes. In this paper, we describe a systematic analysis of putative KPRs in the context of this superfamily. Detailed structural analysis allowed us to define key residues for KPR activity and we classified eight structural genomics structures of the KPR family into four functional subclasses. We proposed a semi-automatic protocol, using sequence-structure homology recognition scores, for assigning KPR and related proteins to these subclasses and applied it to a representative set of 103 completely sequenced bacterial genomes. A similar approach can be applied to other enzyme families, which would aid the correct identification of drug targets and help design novel specific inhibitors.
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Affiliation(s)
- Sukanta Mondal
- National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka, Japan
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14
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Smits SHJ, Meyer T, Mueller A, van Os N, Stoldt M, Willbold D, Schmitt L, Grieshaber MK. Insights into the mechanism of ligand binding to octopine dehydrogenase from Pecten maximus by NMR and crystallography. PLoS One 2010; 5:e12312. [PMID: 20808820 PMCID: PMC2924402 DOI: 10.1371/journal.pone.0012312] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 07/29/2010] [Indexed: 11/18/2022] Open
Abstract
Octopine dehydrogenase (OcDH) from the adductor muscle of the great scallop, Pecten maximus, catalyzes the NADH dependent, reductive condensation of L-arginine and pyruvate to octopine, NAD+, and water during escape swimming and/or subsequent recovery. The structure of OcDH was recently solved and a reaction mechanism was proposed which implied an ordered binding of NADH, L-arginine and finally pyruvate. Here, the order of substrate binding as well as the underlying conformational changes were investigated by NMR confirming the model derived from the crystal structures. Furthermore, the crystal structure of the OcDH/NADH/agmatine complex was determined which suggests a key role of the side chain of L-arginine in protein cataylsis. Thus, the order of substrate binding to OcDH as well as the molecular signals involved in octopine formation can now be described in molecular detail.
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Affiliation(s)
- Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany.
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15
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Smits SHJ, Mueller A, Grieshaber MK, Schmitt L. Coenzyme- and His-tag-induced crystallization of octopine dehydrogenase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:836-9. [PMID: 18765918 DOI: 10.1107/s1744309108025487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 08/07/2008] [Indexed: 05/25/2023]
Abstract
Over the last decade, protein purification has become more efficient and standardized through the introduction of affinity tags. The choice and position of the tag, however, can directly influence the process of protein crystallization. Octopine dehydrogenase (OcDH) without a His tag and tagged protein constructs such as OcDH-His(5) and OcDH-LEHis(6) have been investigated for their crystallizability. Only OcDH-His(5) yielded crystals; however, they were multiple. To improve crystal quality, the cofactor NADH was added, resulting in single crystals that were suitable for structure determination. As shown by the structure, the His(5) tag protrudes into the cleft between the NADH and L-arginine-binding domains and is mainly fixed in place by water molecules. The protein is thereby stabilized to such an extent that the formation of crystal contacts can proceed. Together with NADH, the His(5) tag obviously locks the enzyme into a specific conformation which induces crystal growth.
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Affiliation(s)
- Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
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16
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Smits SHJ, Mueller A, Schmitt L, Grieshaber MK. A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus. J Mol Biol 2008; 381:200-11. [PMID: 18599075 DOI: 10.1016/j.jmb.2008.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 05/26/2008] [Accepted: 06/01/2008] [Indexed: 11/25/2022]
Abstract
Octopine dehydrogenase [N(2)-(D-1-carboxyethyl)-L-arginine:NAD(+) oxidoreductase] (OcDH) from the adductor muscle of the great scallop Pecten maximus catalyzes the reductive condensation of l-arginine and pyruvate to octopine during escape swimming. This enzyme, which is a prototype of opine dehydrogenases (OpDHs), oxidizes glycolytically born NADH to NAD(+), thus sustaining anaerobic ATP provision during short periods of strenuous muscular activity. In contrast to some other OpDHs, OcDH uses only l-arginine as the amino acid substrate. Here, we report the crystal structures of OcDH in complex with NADH and the binary complexes NADH/l-arginine and NADH/pyruvate, providing detailed information about the principles of substrate recognition, ligand binding and the reaction mechanism. OcDH binds its substrates through a combination of electrostatic forces and size selection, which guarantees that OcDH catalysis proceeds with substrate selectivity and stereoselectivity, giving rise to a second chiral center and exploiting a "molecular ruler" mechanism.
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Affiliation(s)
- Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
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17
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Müller A, Janssen F, Grieshaber MK. Putative reaction mechanism of heterologously expressed octopine dehydrogenase from the great scallop, Pecten maximus (L). FEBS J 2007; 274:6329-39. [PMID: 18028427 DOI: 10.1111/j.1742-4658.2007.06151.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
cDNA for octopine dehydrogenase (ODH) from the adductor muscle of the great scallop, Pecten maximus, was cloned using 5'- and 3'-RACE. The cDNA comprises an ORF of 1197 nucleotides and the deduced amino acid sequence encodes a protein of 399 amino acids. ODH was heterologously expressed in Escherichia coli with a C-terminal penta His-tag. ODH-5His was purified to homogeneity using metal-chelate affinity chromatography and Sephadex G-100 gel filtration. Recombinant ODH had kinetic properties similar to those of wild-type ODH isolated from the scallop's adductor muscle. Site-directed mutagenesis was used to elucidate the involvement of several amino acid residues for the reaction catalyzed by ODH. Cys148, which is conserved in all opine dehydrogenases known to date, was converted to serine or alanine, showing that this residue is not intrinsically important for catalysis. His212, Arg324 and Asp329, which are also conserved in all known opine dehydrogenase sequences, were subjected to site-directed mutagenesis. Modification of these residues revealed their importance for the catalytic activity of the enzyme. Conversion of each of these residues to alanine resulted in strong increases in K(m) and decreases in k(cat) values for pyruvate and L-arginine, but had little effect on the K(m) and k(cat) values for NADH. Assuming a similar structure for ODH compared with the only available structure of a bacterial opine dehydrogenase, these three amino acids may function as a catalytic triad in ODH similar to that found in lactate dehydrogenase or malate dehydrogenase. The carboxyl group of pyruvate is then stabilized by Arg324. In addition to orienting the substrate, His212 will act as an acid-base catalyst by donating a proton to the carbonyl group of pyruvate. The acidity of this histidine is further increased by the proximity of Asp329.
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Affiliation(s)
- Andre Müller
- Institut für Zoophysiologie, Heinrich-Heine-Universität, Düsseldorf, Germany.
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18
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Endo N, Kan-no N, Nagahisa E. Purification, characterization, and cDNA cloning of opine dehydrogenases from the polychaete rockworm Marphysa sanguinea. Comp Biochem Physiol B Biochem Mol Biol 2007; 147:293-307. [PMID: 17350870 DOI: 10.1016/j.cbpb.2007.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/18/2007] [Accepted: 01/19/2007] [Indexed: 11/18/2022]
Abstract
Alanopine dehydrogenase (AlDH) and three isoforms of strombine/alanopine dehydrogenase (St/AlDH) were purified from muscle tissue of the polychaete rockworm Marphysa sanguinea. The four enzymes, which can be distinguished by the isoelectric point, are monomeric 42 kDa proteins, possess similar pH-activity profiles, and display specificity for pyruvate and NAD(H). The three isoforms of St/AlDH show equivalent Km and Vmax for glycine and L-alanine and for D-strombine and meso-alanopine. Free amino acid levels in the muscle and D-strombine accumulation in vivo during muscle activity suggest that St/AlDHs function physiologically as StDH. AlDH shows specificity for L-alanine and meso-alanopine, but not for glycine or D-strombine. The amino acid sequences of AlDH and one of the St/AlDH isoforms were determined by a combination of amino acid sequence analysis and cDNA cloning. St/AlDH cDNA consisted of 1586 bp nucleotides that encode a 399-residue protein (43,346.70 Da), and AlDH cDNA consisted of 1587 bp nucleotides that encode a 399-residue protein (43,886.68 Da). The two amino acid sequences deduced from the cDNA displayed 67% amino acid identity, with greatest similarity to that of tauropine dehydrogenase from the polychaete Arabella iricolor.
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Affiliation(s)
- Noriyuki Endo
- Department of Marine Bioscience, School of Fisheries Sciences, Kitasato University, Iwate 022-0101, Japan
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19
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Kan-no N, Endo N, Moriyama S, Nagahisa E, Sato M. The amino acid sequence of tauropine dehydrogenase from the polychaete Arabella iricolor. Comp Biochem Physiol B Biochem Mol Biol 2005; 140:475-85. [PMID: 15694596 DOI: 10.1016/j.cbpc.2004.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Revised: 11/12/2004] [Accepted: 11/15/2004] [Indexed: 10/26/2022]
Abstract
The amino acid sequence of tauropine dehydrogenase (EC 1.5.1.23) from the polychaete Arabella iricolor was determined by automated sequencing of fragments obtained by cleavage with lysyl endopeptidase, endoproteinase Glu-C, and cyanogen bromide. The purified enzyme contained two isoforms that differ only in the 41st amino acid residue (Thr or Ile). Although the sequence contained eight Cys residues, intrachain disulfide bonds were not found. Two possible N-linked glycosylation sites occur in the sequences, but the enzyme does not appear to contain bound carbohydrates. Based on these data, the two isoforms of Arabella tauropine dehydrogenase are simple proteins consisted of 396 amino acid residues with calculated molecular masses of 43,085.7 Da (Thr41 isoform) and 43,097.8 Da (Ile41 isoform).
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Affiliation(s)
- Nobuhiro Kan-no
- Department of Marine Biosciences, School of Fisheries Sciences, Kitasato University, Sanriku 160-4, Ohfunato, Iwate 022-0101, Japan.
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20
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Videau LL, Arendall WB, Richardson JS. The cis-Pro touch-turn: a rare motif preferred at functional sites. Proteins 2004; 56:298-309. [PMID: 15211513 DOI: 10.1002/prot.20101] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A new motif of three-dimensional (3D) protein structure is described, called the cis-Pro touch-turn. In this four-residue, three-peptide motif, the central peptide is cis. Residue 2, which precedes the proline, has phi, psi values either in the "prePro region" of the Ramachandran plot near -130 degrees, 75 degrees or in the Lalpha region near +60 degrees, +60 degrees. The Calpha(1)-Calpha(4) distance is 4-5 A and the two flanking peptides lie parallel to one another, making van der Waals contact rather than a hydrogen bond. Apparently, this arrangement is locally unfavorable and therefore rare, usually occurring only if needed for biological function. Of the 12 examples in a 500-protein database, cis-Pro touch-turns are found at the catalytic sites of pectate lyase, Ni-Fe hydrogenase, glucoamylase, xylanase, and opine dehydrogenase and at the primary binding sites of ribonuclease H, type I DNA polymerase, ribotoxin, and phage gene 3 protein. In each of these protein families, the touch-turns serve different roles; their functional importance is supported by conservation and mutagenesis data. In analyzing the conservation patterns of these 3D motifs, new methods for in-depth quality evaluation of the structural bioinformatic data are employed to distinguish between significant exceptions and errors
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Affiliation(s)
- Lizbeth L Videau
- Department of Biochemistry, Duke University, Durham, North Carolina 27710-3711, USA
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21
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Kimura T, Nakano T, Yamaguchi T, Sato M, Ogawa T, Muramoto K, Yokoyama T, Kan-No N, Nagahisa E, Janssen F, Grieshaber MK. Complementary DNA cloning and molecular evolution of opine dehydrogenases in some marine invertebrates. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2004; 6:493-502. [PMID: 15565272 DOI: 10.1007/s10126-004-2700-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2003] [Accepted: 02/23/2004] [Indexed: 05/24/2023]
Abstract
The complete complementary DNA sequences of genes presumably coding for opine dehydrogenases from Arabella iricolor (sandworm), Haliotis discus hannai (abalone), and Patinopecten yessoensis (scallop) were determined, and partial cDNA sequences were derived for Meretrix lusoria (Japanese hard clam) and Spisula sachalinensis (Sakhalin surf clam). The primers ODH-9F and ODH-11R proved useful for amplifying the sequences for opine dehydrogenases from the 4 mollusk species investigated in this study. The sequence of the sandworm was obtained using primers constructed from the amino acid sequence of tauropine dehydrogenase, the main opine dehydrogenase in A. iricolor. The complete cDNA sequence of A. iricolor, H. discus hannai, and P. yessoensis encode 397, 400, and 405 amino acids, respectively. All sequences were aligned and compared with published databank sequences of Loligo opalescens, Loligo vulgaris (squid), Sepia officinalis (cuttlefish), and Pecten maximus (scallop). As expected, a high level of homology was observed for the cDNA from closely related species, such as for cephalopods or scallops, whereas cDNA from the other species showed lower-level homologies. A similar trend was observed when the deduced amino acid sequences were compared. Furthermore, alignment of these sequences revealed some structural motifs that are possibly related to the binding sites of the substrates. The phylogenetic trees derived from the nucleotide and amino acid sequences were consistent with the classification of species resulting from classical taxonomic analyses.
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Affiliation(s)
- Tomohiro Kimura
- Laboratory of Marine Biochemistry, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
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22
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Choe J, Guerra D, Michels PAM, Hol WGJ. Leishmania mexicana glycerol-3-phosphate dehydrogenase showed conformational changes upon binding a bi-substrate adduct. J Mol Biol 2003; 329:335-49. [PMID: 12758080 DOI: 10.1016/s0022-2836(03)00421-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Certain pathogenic trypanosomatids are highly dependent on glycolysis for ATP production, and hence their glycolytic enzymes, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. The ternary complex structure of Leishmania mexicana GPDH (LmGPDH) with dihydroxyacetone phosphate (DHAP) and NAD(+) was determined to 1.9A resolution as a further step towards understanding this enzyme's mode of action. When compared with the apo and binary complex structures, the ternary complex structure shows an 11 degrees hinge-bending motion of the C-terminal domain with respect to the N-terminal domain. In addition, residues in the C-terminal domain involved in catalysis or substrates binding show significant movements and a previously invisible five-residue loop region becomes well ordered and participates in NAD(+) binding. Unexpectedly, DHAP and NAD(+) appear to form a covalent bond, producing an adduct in the active site of LmGPDH. Modeling a ternary complex glycerol 3-phosphate (G3P) and NAD(+) with LmGPDH identified ten active site residues that are highly conserved among all GPDHs. Two lysine residues, Lys125 and Lys210, that are presumed to be critical in catalysis, were mutated resulting in greatly reduced catalytic activity. Comparison with other structurally related enzymes found by the program DALI suggested Lys210 as a key catalytic residue, which is located on a structurally conserved alpha-helix. From the results of site-directed mutagenesis, molecular modeling and comparison with related dehydrogenases, a catalytic mechanism of LmGPDH and a possible evolutionary scenario of this group of dehydrogenases are proposed.
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Affiliation(s)
- Jungwoo Choe
- Department of Biochemistry, Biomolecular Structure and Design program, University of Washington, Seattle 98195-7742, USA
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23
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Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK. Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase: evidence for a very divergent long-chain dehydrogenase family. Chem Biol Interact 2003; 143-144:551-8. [PMID: 12604241 DOI: 10.1016/s0009-2797(02)00218-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mannitol 2-dehydrogenase from Pseudomonas fluorescens (pfMDH) is a secondary alcohol dehydrogenase that catalyzes the reversible NAD(P)-dependent oxidation of D-mannitol to D-fructose, D-arabinitol to D-xylulose, and D-sorbitol to L-sorbose. It is a member of the mostly prokaryotic family of long-chain mannitol dehydrogenases that so far includes 66 members. Unlike other alcohol and polyol dehydrogenases that utilize metal cofactors or a conserved active-site tyrosine for catalysis, an invariant lysine is the general base. The crystal structure of pfMDH in a binary complex with NAD(H) and a ternary complex with NAD(H) and D-mannitol have been determined to 1.7 and 1.8 A resolution respectively. Comparison of secondary structure assignment to sequence alignments suggest the shortest members of this family, mannitol-1-phosphate 5-dehydrogenases, retain core elements but lack secondary structural components found on the surface of pfMDH. The elements predicted to be absent are distributed throughout the primary sequence, implying that a simple truncation or fusion did not occur. The closest structural neighbors are 6-phosphogluconate dehydrogenase, UDP-glucose dehydrogenase, N-(1-D-carboxyethyl)-L-norvaline dehydrogenase, and glycerol-3-phosphate dehydrogenase. Although sequence identity is only a barely recognizable 7-10%, conservation of secondary structural elements as well as homologous residues that are contributed to the active site indicates they may be related by divergent evolution.
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Affiliation(s)
- Kathryn L Kavanagh
- Section of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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24
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Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK. Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism. J Biol Chem 2002; 277:43433-42. [PMID: 12196534 DOI: 10.1074/jbc.m206914200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Long-chain mannitol dehydrogenases are secondary alcohol dehydrogenases that are of wide interest because of their involvement in metabolism and potential applications in agriculture, medicine, and industry. They differ from other alcohol and polyol dehydrogenases because they do not contain a conserved tyrosine and are not dependent on Zn(2+) or other metal cofactors. The structures of the long-chain mannitol 2-dehydrogenase (54 kDa) from Pseudomonas fluorescens in a binary complex with NAD(+) and ternary complex with NAD(+) and d-mannitol have been determined to resolutions of 1.7 and 1.8 A and R-factors of 0.171 and 0.176, respectively. These results show an N-terminal domain that includes a typical Rossmann fold. The C-terminal domain is primarily alpha-helical and mediates mannitol binding. The electron lone pair of Lys-295 is steered by hydrogen-bonding interactions with the amide oxygen of Asn-300 and the main-chain carbonyl oxygen of Val-229 to act as the general base. Asn-191 and Asn-300 are involved in a web of hydrogen bonding, which precisely orients the mannitol O2 proton for abstraction. These residues also aid in stabilizing a negative charge in the intermediate state and in preventing the formation of nonproductive complexes with the substrate. The catalytic lysine may be returned to its unprotonated state using a rectifying proton tunnel driven by Glu-292 oscillating among different environments. Despite low sequence homology, the closest structural neighbors are glycerol-3-phosphate dehydrogenase, N-(1-d-carboxylethyl)-l-norvaline dehydrogenase, UDP-glucose dehydrogenase, and 6-phosphogluconate dehydrogenase, indicating a possible evolutionary relationship among these enzymes.
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Affiliation(s)
- Kathryn L Kavanagh
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
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Abstract
Most proteins in genomes are the result of the recombination of two or more domains. It has been found that if proteins are formed by a combination of domains from superfamilies A and B, then the domains may occur in the sequential order AB or BA but only in about 2% of cases do they occur in both sequential orders. The classical Rossmann domains of known structure are combined with catalytic domains from seven different superfamilies. In addition, there are eight cases where structures with both AB and BA domain combinations are known. For these two sets of structures, we analysed: (i) the relative orientation of the domains; (ii) the type of domain connection; (iii) the structure of the interdomain links; and (iv) domain function. The results of this analysis indicate that in most cases domain order is conserved because recombination of the domains has only occurred once during the course of evolution. Functional reasons become important when the domain connections are short. In seven out of the eight known cases where domains are combined in the AB and BA sequential orders they have different geometrical relationships that give them different functional properties.
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Affiliation(s)
- Matthew Bashton
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England.
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26
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Warkentin E, Mamat B, Sordel-Klippert M, Wicke M, Thauer RK, Iwata M, Iwata S, Ermler U, Shima S. Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound. EMBO J 2001; 20:6561-9. [PMID: 11726492 PMCID: PMC125772 DOI: 10.1093/emboj/20.23.6561] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2001] [Revised: 10/02/2001] [Accepted: 10/18/2001] [Indexed: 11/12/2022] Open
Abstract
Cofactor F420 is a 5'-deazaflavin derivative first discovered in methanogenic archaea but later found also to be present in some bacteria. As a coenzyme, it is involved in hydride transfer reactions and as a prosthetic group in the DNA photolyase reaction. We report here for the first time on the crystal structure of an F420-dependent oxidoreductase bound with F420. The structure of F420H2:NADP+ oxidoreductase resolved to 1.65 A contains two domains: an N-terminal domain characteristic of a dinucleotide-binding Rossmann fold and a smaller C-terminal domain. The nicotinamide and the deazaflavin part of the two coenzymes are bound in the cleft between the domains such that the Si-faces of both face each other at a distance of 3.1 A, which is optimal for hydride transfer. Comparison of the structures bound with and without substrates reveals that of the two substrates NADP has to bind first, the binding being associated with an induced fit.
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Affiliation(s)
- Eberhard Warkentin
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Björn Mamat
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Melanie Sordel-Klippert
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Michaela Wicke
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Rudolf K. Thauer
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Momi Iwata
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - So Iwata
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
| | - Seigo Shima
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany and Department of Biological Sciences and Division of Biomedical Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK Corresponding authors e-mail: , or
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Ruvinov SB, Thompson J, Sackett DL, Ginsburg A. Tetrameric N(5)-(L-1-carboxyethyl)-L-ornithine synthase: guanidine. HCl-induced unfolding and a low temperature requirement for refolding. Arch Biochem Biophys 1999; 371:115-23. [PMID: 10525296 DOI: 10.1006/abbi.1999.1429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Guanidine x HCl (GdnHCl)-induced unfolding of tetrameric N(5)-(L-1-carboxyethyl)-L-ornithine synthase (CEOS; 141,300 M(r)) from Lactococcus lactis at pH 7.2 and 25 degrees C occurred in several phases. The enzyme was inactivated at approximately 1 M GdnHCl. A time-, temperature-, and concentration-dependent formation of soluble protein aggregates occurred at 0.5-1.5 M GdnHCl due to an increased exposure of apolar surfaces. A transition from tetramer to unfolded monomer was observed between 2 and 3.5 M GdnHCl (without observable dimer or trimer intermediates), as evidenced by tyrosyl and tryptophanyl fluorescence changes, sulfhydryl group exposure, loss of secondary structure, size-exclusion chromatography, and sedimentation equilibrium data. GdnHCl-induced dissociation and unfolding of tetrameric CEOS was concerted, and yields of reactivated CEOS by dilution from 5 M GdnHCl were improved when unfolding took place on ice rather than at 25 degrees C. Refolding and reconstitution of the enzyme were optimal at </=15 degrees C and yields of active tetramer increased as the concentration of unfolded subunits decreased. Refolding of unfolded subunits and active tetramer assembly upon 100-fold dilution from 5 M GdnHCl at 0 degrees C also was increased two- or fourfold (to 44 or 28% reactivation for 0.08 or 0.28 microM subunit, respectively) when incubated at 15 degrees C, pH 7.2, for 4 h with the Escherichia coli molecular chaperonin GroEL, ATP, MgCl(2), and KCl.
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Affiliation(s)
- S B Ruvinov
- Laboratory of Biochemistry, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
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28
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Sackett DL, Ruvinov SB, Thompson J. N5-(L-1-carboxyethyl)-L-ornithine synthase: physical and spectral characterization of the enzyme and its unusual low pKa fluorescent tyrosine residues. Protein Sci 1999; 8:2121-9. [PMID: 10548058 PMCID: PMC2144144 DOI: 10.1110/ps.8.10.2121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
N5-(L-1-carboxyethyl)-L-ornithine synthase [E.C. 1.5.1.24] (CEOS) from Lactococcus lactis has been cloned, expressed, and purified from Escherichia coli in quantities sufficient for characterization by biophysical methods. The NADPH-dependent enzyme is a homotetramer (Mr approximately equal to 140,000) and in the native state is stabilized by noncovalent interactions between the monomers. The far-ultraviolet circular dichroism spectrum shows that the folding pattern of the enzyme is typical of the alpha,beta family of proteins. CEOS contains one tryptophan (Trp) and 19 tyrosines (Tyr) per monomer, and the fluorescence spectrum of the protein shows emission from both Trp and Tyr residues. Relative to N-acetyltyrosinamide, the Tyr quantum yield of the native enzyme is about 0.5. All 19 Tyr residues are titratable and, of these, two exhibit the uncommonly low pKa of approximately 8.5, 11 have pKa approximately 10.75, and the remaining six titrate with pKa approximately 11.3. The two residues with pKa approximately 8.5 contribute approximately 40% of the total tyrosine emission, implying a relative quantum yield >1, probably indicating Tyr-Tyr energy transfer. In the presence of NADPH, Tyr fluorescence is reduced by 40%, and Trp fluorescence is quenched completely. The latter result suggests that the single Trp residue is either at the active site, or in proximity to the sequence GSGNVA, that constitutes the beta alphabeta fold of the nucleotide-binding domain. Chymotrypsin specifically cleaves native CEOS after Phe255. Although inactivated by this single-site cleavage of the subunit, the enzyme retains the capacity to bind NADPH and tetramer stability is maintained. Possible roles in catalysis for the chymotrypsin sensitive loop and for the low pKa Tyr residues are discussed.
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Affiliation(s)
- D L Sackett
- Laboratory of Integrative and Medical Biophysics, NICHD, National Institutes of Health, Bethesda, Maryland 20892-4855, USA.
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Liddington R, Frederick C. Paper Alert. Structure 1998. [DOI: 10.1016/s0969-2126(98)00121-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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