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Timucin E, Cousido-Siah A, Mitschler A, Podjarny A, Sezerman OU. Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5. Proteins 2015; 84:129-42. [DOI: 10.1002/prot.24961] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/09/2015] [Accepted: 11/06/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Emel Timucin
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering; Sabanci University; Istanbul 34956 Turkey
| | - Alexandra Cousido-Siah
- Department of Integrative Biology; Institut De Génétique Et De Biologie Moléculaire Et Cellulaire, CNRS, INSERM, UdS; 1 Rue Laurent Fries, 67404 Illkirch Cedex France
| | - André Mitschler
- Department of Integrative Biology; Institut De Génétique Et De Biologie Moléculaire Et Cellulaire, CNRS, INSERM, UdS; 1 Rue Laurent Fries, 67404 Illkirch Cedex France
| | - Alberto Podjarny
- Department of Integrative Biology; Institut De Génétique Et De Biologie Moléculaire Et Cellulaire, CNRS, INSERM, UdS; 1 Rue Laurent Fries, 67404 Illkirch Cedex France
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine; Acibadem University; Atasehir Istanbul 34742 Turkey
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Benavente R, Esteban-Torres M, Kohring GW, Cortés-Cabrera Á, Sánchez-Murcia PA, Gago F, Acebrón I, de las Rivas B, Muñoz R, Mancheño JM. Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli. ACTA ACUST UNITED AC 2015; 71:1540-54. [PMID: 26143925 DOI: 10.1107/s1399004715009281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/15/2015] [Indexed: 11/11/2022]
Abstract
Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that belongs to the medium-chain dehydrogenase/reductase (MDR) superfamily. It catalyses the Zn(2+)- and NAD(+)-dependent stereoselective dehydrogenation of L-galactitol 1-phosphate to D-tagatose 6-phosphate. Here, three crystal structures of GPDH from Escherichia coli are reported: that of the open state of GPDH with Zn(2+) in the catalytic site and those of the closed state in complex with the polyols Tris and glycerol, respectively. The closed state of GPDH reveals no bound cofactor, which is at variance with the conformational transition of the prototypical mammalian liver alcohol dehydrogenase. The main intersubunit-contacting interface within the GPDH homodimer presents a large internal cavity that probably facilitates the relative movement between the subunits. The substrate analogue glycerol bound within the active site partially mimics the catalytically relevant backbone of galactitol 1-phosphate. The glycerol binding mode reveals, for the first time in the polyol dehydrogenases, a pentacoordinated zinc ion in complex with a polyol and also a strong hydrogen bond between the primary hydroxyl group and the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue.
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Affiliation(s)
- Rocío Benavente
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Esteban-Torres
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Gebäude A1.5, 66123 Saarbruecken, Germany
| | - Álvaro Cortés-Cabrera
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Federico Gago
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Blanca de las Rivas
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Rosario Muñoz
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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Nealon CM, Musa MM, Patel JM, Phillips RS. Controlling Substrate Specificity and Stereospecificity of Alcohol Dehydrogenases. ACS Catal 2015. [DOI: 10.1021/cs501457v] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher M. Nealon
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Musa M. Musa
- Department
of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
| | - Jay M. Patel
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Robert S. Phillips
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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Molecular analysis of hyperthermophilic endoglucanase Cel12B from Thermotoga maritima and the properties of its functional residues. BMC STRUCTURAL BIOLOGY 2014; 14:8. [PMID: 24529187 PMCID: PMC3936955 DOI: 10.1186/1472-6807-14-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/13/2014] [Indexed: 12/30/2022]
Abstract
Background Although many hyperthermophilic endoglucanases have been reported from archaea and bacteria, a complete survey and classification of all sequences in these species from disparate evolutionary groups, and the relationship between their molecular structures and functions are lacking. The completion of several high-quality gene or genome sequencing projects provided us with the unique opportunity to make a complete assessment and thorough comparative analysis of the hyperthermophilic endoglucanases encoded in archaea and bacteria. Results Structure alignment of the 19 hyperthermophilic endoglucanases from archaea and bacteria which grow above 80°C revealed that Gly30, Pro63, Pro83, Trp115, Glu131, Met133, Trp135, Trp175, Gly227 and Glu229 are conserved amino acid residues. In addition, the average percentage composition of residues cysteine and histidine of 19 endoglucanases is only 0.28 and 0.74 while it is high in thermophilic or mesophilic one. It can be inferred from the nodes that there is a close relationship among the 19 protein from hyperthermophilic bacteria and archaea based on phylogenetic analysis. Among these conserved amino acid residues, as far as Cel12B concerned, two Glu residues might be the catalytic nucleophile and proton donor, Gly30, Pro63, Pro83 and Gly227 residues might be necessary to the thermostability of protein, and Trp115, Met133, Trp135, Trp175 residues is related to the binding of substrate. Site-directed mutagenesis results reveal that Pro63 and Pro83 contribute to the thermostability of Cel12B and Met133 is confirmed to have role in enhancing the binding of substrate. Conclusions The conserved acids have been shown great importance to maintain the structure, thermostability, as well as the similarity of the enzymatic properties of those proteins. We have made clear the function of these conserved amino acid residues in Cel12B protein, which is helpful in analyzing other undetailed molecular structure and transforming them with site directed mutagenesis, as well as providing the theoretical basis for degrading cellulose from woody and herbaceous plants.
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Jakoblinnert A, van den Wittenboer A, Shivange AV, Bocola M, Heffele L, Ansorge-Schumacher M, Schwaneberg U. Design of an activity and stability improved carbonyl reductase from Candida parapsilosis. J Biotechnol 2013; 165:52-62. [DOI: 10.1016/j.jbiotec.2013.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
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Thermostable alcohol dehydrogenase from Thermococcus kodakarensis KOD1 for enantioselective bioconversion of aromatic secondary alcohols. Appl Environ Microbiol 2013; 79:2209-17. [PMID: 23354700 DOI: 10.1128/aem.03873-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel thermostable alcohol dehydrogenase (ADH) showing activity toward aromatic secondary alcohols was identified from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkADH). The gene, tk0845, which encodes an aldo-keto reductase, was heterologously expressed in Escherichia coli. The enzyme was found to be a monomer with a molecular mass of 31 kDa. It was highly thermostable with an optimal temperature of 90°C and a half-life of 4.5 h at 95°C. The apparent K(m) values for the cofactors NAD(P)(+) and NADPH were similar within a range of 66 to 127 μM. TkADH preferred secondary alcohols and accepted various ketones and aldehydes as substrates. Interestingly, the enzyme could oxidize 1-phenylethanol and its derivatives having substituents at the meta and para positions with high enantioselectivity, yielding the corresponding (R)-alcohols with optical purities of greater than 99.8% enantiomeric excess (ee). TkADH could also reduce 2,2,2-trifluoroacetophenone to (R)-2,2,2-trifluoro-1-phenylethanol with high enantioselectivity (>99.6% ee). Furthermore, the enzyme showed high resistance to organic solvents and was particularly highly active in the presence of H2O-20% 2-propanol and H2O-50% n-hexane or n-octane. This ADH is expected to be a useful tool for the production of aromatic chiral alcohols.
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Jakoblinnert A, Wachtmeister J, Schukur L, Shivange AV, Bocola M, Ansorge-Schumacher MB, Schwaneberg U. Reengineered carbonyl reductase for reducing methyl-substituted cyclohexanones. Protein Eng Des Sel 2013; 26:291-8. [DOI: 10.1093/protein/gzt001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Liu X, Bastian S, Snow CD, Brustad EM, Saleski TE, Xu JH, Meinhold P, Arnold FH. Structure-guided engineering of Lactococcus lactis alcohol dehydrogenase LlAdhA for improved conversion of isobutyraldehyde to isobutanol. J Biotechnol 2012; 164:188-95. [PMID: 22974724 PMCID: PMC3542407 DOI: 10.1016/j.jbiotec.2012.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/14/2012] [Accepted: 08/20/2012] [Indexed: 11/17/2022]
Abstract
We have determined the X-ray crystal structures of the NADH-dependent alcohol dehydrogenase LlAdhA from Lactococcus lactis and its laboratory-evolved variant LlAdhA(RE1) at 1.9Å and 2.5Å resolution, respectively. LlAdhA(RE1), which contains three amino acid mutations (Y50F, I212T, and L264V), was engineered to increase the microbial production of isobutanol (2-methylpropan-1-ol) from isobutyraldehyde (2-methylpropanal). Structural comparison of LlAdhA and LlAdhA(RE1) indicates that the enhanced activity on isobutyraldehyde stems from increases in the protein's active site size, hydrophobicity, and substrate access. Further structure-guided mutagenesis generated a quadruple mutant (Y50F/N110S/I212T/L264V), whose KM for isobutyraldehyde is ∼17-fold lower and catalytic efficiency (kcat/KM) is ∼160-fold higher than wild-type LlAdhA. Combining detailed structural information and directed evolution, we have achieved significant improvements in non-native alcohol dehydrogenase activity that will facilitate the production of next-generation fuels such as isobutanol from renewable resources.
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Affiliation(s)
- Xiang Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Sabine Bastian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Christopher D. Snow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Eric M. Brustad
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Tatyana E. Saleski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peter Meinhold
- Gevo, Inc., 345 Inverness Drive S., Buiding C, Suite 310, Englewood, CO 80112, USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
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Zhu J, Shi J, Pan Z. Purification and characterization of a hexanol-degrading enzyme extracted from apple. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3246-3252. [PMID: 22332825 DOI: 10.1021/jf204548r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
An enzyme having activity toward n-hexanol was purified from apple, and its biochemical characteristics were analyzed. The purification steps consisted of sedimentation with ammonium sulfate, DEAE Sepharose Fast Flow ion exchange chromatography, and Sephadex G-100 column. The obtained enzyme had a yield of 16.00% with a specific activity of 18879.20 U/mg protein and overall purification of 142.77-fold. The enzyme showed activity to isoamylol, 1-propanol, n-hexanol, and isobutanol but not toward methanol and ethanol. With n-hexanol as a substrate, the optimum conditions were pH 4.0 and 30 °C for enzyme activity and pH 3.0-4.0 and temperatures below 40 °C for enzyme stability. The enzyme activity was increased significantly by adding l-cysteine and Fe(2+) at all tested concentrations and slightly by Zn(2+) at a high concentration but decreased by additions of EDTA, Ga(2+), K(+), Mg(2+), sodium dodecyl sulfate (SDS), sodium aluminum sulfate (SAS), dithiothreitol (DTT), and glutathione (GSH). The enzyme activities toward n-hexanol and n-hexanal were increased by NADH but decreased by NAD(+), in contrast to a decrease toward n-hexane by addition of both NAD(+) and NADH.
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Affiliation(s)
- Jing Zhu
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi Province, 712100, China
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Applegate GA, Cheloha RW, Nelson DL, Berkowitz DB. A new dehydrogenase from Clostridium acetobutylicum for asymmetric synthesis: dynamic reductive kinetic resolution entry into the Taxotère side chain. Chem Commun (Camb) 2011; 47:2420-2. [PMID: 21173953 PMCID: PMC4882475 DOI: 10.1039/c0cc04585c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An NADP-dependent alcohol dehydrogenase from Clostridium acetobutylicum (CaADH) has been expressed and characterized. CaADH enantioselectively reduces aromatic α-, β- and γ-keto esters to the corresponding D-hydroxy esters and provides a building block for the Taxotère side chain (95% yield, 95% de, 99% ee) by dynamic reductive kinetic resolution (DYRKR).
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Affiliation(s)
- Gregory A. Applegate
- Department of Chemistry &,Nebraska Center for Energy Sciences Research (NCESR), University of Nebraska, Lincoln, NE USA. Fax: 01 402 472 9402; 01 402 472 2738
| | - Ross W. Cheloha
- Department of Chemistry &,Nebraska Center for Energy Sciences Research (NCESR), University of Nebraska, Lincoln, NE USA. Fax: 01 402 472 9402; 01 402 472 2738
| | - David L. Nelson
- Department of Chemistry &,Nebraska Center for Energy Sciences Research (NCESR), University of Nebraska, Lincoln, NE USA. Fax: 01 402 472 9402; 01 402 472 2738
| | - David B. Berkowitz
- Department of Chemistry &,Nebraska Center for Energy Sciences Research (NCESR), University of Nebraska, Lincoln, NE USA. Fax: 01 402 472 9402; 01 402 472 2738
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