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Fahmi Himo - One of the best experts on this subject based on the ideXlab platform.

  • Catalytic Mechanism of Limonene Epoxide Hydrolase, a Theoretical Study
    Journal of the American Chemical Society, 2005
    Co-Authors: Kathrin H. Hopmann, B. Martin Hallberg, Fahmi Himo
    Abstract:

    The Catalytic Mechanism of limonene epoxide hydrolase (LEH) was investigated theoretically using the density functional theory method B3LYP. LEH is part of a novel limonene degradation pathway foun ...

  • Catalytic Mechanism of pyruvate formate lyase revisited
    Journal of Physical Chemistry B, 2004
    Co-Authors: Fahmi Himo
    Abstract:

    The Catalytic Mechanism of the glycyl-radical-containing enzyme pyruvate-formate lyase (PFL) is investigated using high-level quantum chemical methods. PFL catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetylated CoA. Large models are employed, based on a recent X-ray crystal structure of PFL in complex with the pyruvate substrate. The rate-limiting step is shown to be the homolytic C1-C2 bond cleavage of pyruvate, which occurs after the attack of the Cys418 radical on the carbonyl carbon of pyruvate. For the acetylation of CoA, we propose a new Mechanism, in which the released formyl radical anion abstracts a hydrogen atom directly from CoA. This way, the acetyl group transfer from Cys418 becomes facile. The full potential energy curve for the PFL reactions is presented.

  • Catalytic Mechanism of Pyruvate−Formate Lyase Revisited
    Journal of Physical Chemistry B, 2004
    Co-Authors: Fahmi Himo
    Abstract:

    The Catalytic Mechanism of the glycyl-radical-containing enzyme pyruvate-formate lyase (PFL) is investigated using high-level quantum chemical methods. PFL catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetylated CoA. Large models are employed, based on a recent X-ray crystal structure of PFL in complex with the pyruvate substrate. The rate-limiting step is shown to be the homolytic C1-C2 bond cleavage of pyruvate, which occurs after the attack of the Cys418 radical on the carbonyl carbon of pyruvate. For the acetylation of CoA, we propose a new Mechanism, in which the released formyl radical anion abstracts a hydrogen atom directly from CoA. This way, the acetyl group transfer from Cys418 becomes facile. The full potential energy curve for the PFL reactions is presented.

  • Catalytic Mechanism OF PYRUVATE FORMATE-LYASE (PFL). A THEORETICAL STUDY
    Journal of the American Chemical Society, 1998
    Co-Authors: Fahmi Himo, Leif A Eriksson
    Abstract:

    Pyruvate formate-lyase (PFL) is a glycyl radical containing enzyme that catalyzes the reversible CoA-dependent conversion of pyruvate into acetyl-CoA and formate. We have studied the Catalytic Mechanism of this enzyme by means of accurate quantum chemical methods. It is shown that an overall homolytic radical Mechanism is very feasible. In particular, the formation of a tetrahedral radical intermediate, by addition of thiyl radical to pyruvate, is supported by the calculated reaction energies and barriers. Furthermore, we propose that the thioester exchange between active site cysteine and CoA proceeds via a radical Mechanism. This is made possible by the quenching of the formate radical by Cys418, and not Gly734, as previously proposed.

Lichun Qian - One of the best experts on this subject based on the ideXlab platform.

  • a novel glycoside hydrolase family 113 endo β 1 4 mannanase from alicyclobacillus sp strain a4 and insight into the substrate recognition and Catalytic Mechanism of this family
    Applied and Environmental Microbiology, 2016
    Co-Authors: Haiqiang Lu, Lichun Qian
    Abstract:

    ABSTRACT Few members of glycoside hydrolase (GH) family 113 have been characterized, and information on substrate recognition by and the Catalytic Mechanism of this family is extremely limited. In the present study, a novel endo-β-1,4-mannanase of GH 113, Man113A, was identified in thermoacidophilic Alicyclobacillus sp. strain A4 and found to exhibit both hydrolytic and transglycosylation activities. The enzyme had a broad substrate spectrum, showed higher activities on glucomannan than on galactomannan, and released mannobiose and mannotriose as the main hydrolysis products after an extended incubation. Compared to the only functionally characterized and structure-resolved counterpart Alicyclobacillus acidocaldarius ManA ( Aa ManA) of GH 113, Man113A showed much higher Catalytic efficiency on mannooligosaccharides, in the order mannohexaose ≈ mannopentaose > mannotetraose > mannotriose, and required at least four sugar units for efficient catalysis. Homology modeling, molecular docking analysis, and site-directed mutagenesis revealed the vital roles of eight residues (Trp13, Asn90, Trp96, Arg97, Tyr196, Trp274, Tyr292, and Cys143) related to substrate recognition by and Catalytic Mechanism of GH 113. Comparison of the binding pockets and key residues of β-mannanases of different families indicated that members of GH 113 and GH 5 have more residues serving as stacking platforms to support −4 to −1 subsites than those of GH 26 and that the residues preceding the acid/base catalyst are quite different. Taken as a whole, this study elucidates substrate recognition by and the Catalytic Mechanism of GH 113 β-mannanases and distinguishes them from counterparts of other families.

  • A novel glycoside hydrolase family 113 endo-β-1,4-mannanase from Alicyclobacillus sp. strain A4 and insight into the substrate recognition and Catalytic Mechanism of this family
    Applied and Environmental Microbiology, 2016
    Co-Authors: Wei Xia, Haiqiang Lu, Mengjuan Xia, Lichun Qian, Pengjun Shi, Huiying Luo, Yingguo Bai, Ying Cui, Bin Yao
    Abstract:

    © 2016, American Society for Microbiology. All Rights Reserved.Few members of glycoside hydrolase (GH) family 113 have been characterized, and information on substrate recognition by and the Catalytic Mechanism of this family is extremely limited. In the present study, a novel endo-β-1,4-mannanase of GH 113, Man113A, was identified in thermoacidophilic Alicyclobacillus sp. strain A4 and found to exhibit both hydrolytic and transglycosylation activities. The enzyme had a broad substrate spectrum, showed higher activities on glucomannan than on galactomannan, and released mannobiose and mannotriose as the main hydrolysis products after an extended incubation. Compared to the only functionally characterized and structure-resolved counterpart Alicyclobacillus acidocaldarius ManA (AaManA) of GH 113, Man113A showed much higher Catalytic efficiency on mannooligosaccharides, in the order mannohexaose ≈ mannopentaose > mannotetraose > mannotriose, and required at least four sugar units for efficient catalysis. Homology modeling, molecular docking analysis, and site-directed mutagenesis revealed the vital roles of eight residues (Trp13, Asn90, Trp96, Arg97, Tyr196, Trp274, Tyr292, and Cys143) related to substrate recognition by and Catalytic Mechanism of GH 113. Comparison of the binding pockets and key residues of β-mannanases of different families indicated that members of GH 113 and GH 5 have more residues serving as stacking platforms to support -4 to -1 subsites than those of GH 26 and that the residues preceding the acid/base catalyst are quite different. Taken as a whole, this study elucidates substrate recognition by and the Catalytic Mechanism of GH 113 β-mannanases and distinguishes them from counterparts of other families.

Haiqiang Lu - One of the best experts on this subject based on the ideXlab platform.

  • a novel glycoside hydrolase family 113 endo β 1 4 mannanase from alicyclobacillus sp strain a4 and insight into the substrate recognition and Catalytic Mechanism of this family
    Applied and Environmental Microbiology, 2016
    Co-Authors: Haiqiang Lu, Lichun Qian
    Abstract:

    ABSTRACT Few members of glycoside hydrolase (GH) family 113 have been characterized, and information on substrate recognition by and the Catalytic Mechanism of this family is extremely limited. In the present study, a novel endo-β-1,4-mannanase of GH 113, Man113A, was identified in thermoacidophilic Alicyclobacillus sp. strain A4 and found to exhibit both hydrolytic and transglycosylation activities. The enzyme had a broad substrate spectrum, showed higher activities on glucomannan than on galactomannan, and released mannobiose and mannotriose as the main hydrolysis products after an extended incubation. Compared to the only functionally characterized and structure-resolved counterpart Alicyclobacillus acidocaldarius ManA ( Aa ManA) of GH 113, Man113A showed much higher Catalytic efficiency on mannooligosaccharides, in the order mannohexaose ≈ mannopentaose > mannotetraose > mannotriose, and required at least four sugar units for efficient catalysis. Homology modeling, molecular docking analysis, and site-directed mutagenesis revealed the vital roles of eight residues (Trp13, Asn90, Trp96, Arg97, Tyr196, Trp274, Tyr292, and Cys143) related to substrate recognition by and Catalytic Mechanism of GH 113. Comparison of the binding pockets and key residues of β-mannanases of different families indicated that members of GH 113 and GH 5 have more residues serving as stacking platforms to support −4 to −1 subsites than those of GH 26 and that the residues preceding the acid/base catalyst are quite different. Taken as a whole, this study elucidates substrate recognition by and the Catalytic Mechanism of GH 113 β-mannanases and distinguishes them from counterparts of other families.

  • A novel glycoside hydrolase family 113 endo-β-1,4-mannanase from Alicyclobacillus sp. strain A4 and insight into the substrate recognition and Catalytic Mechanism of this family
    Applied and Environmental Microbiology, 2016
    Co-Authors: Wei Xia, Haiqiang Lu, Mengjuan Xia, Lichun Qian, Pengjun Shi, Huiying Luo, Yingguo Bai, Ying Cui, Bin Yao
    Abstract:

    © 2016, American Society for Microbiology. All Rights Reserved.Few members of glycoside hydrolase (GH) family 113 have been characterized, and information on substrate recognition by and the Catalytic Mechanism of this family is extremely limited. In the present study, a novel endo-β-1,4-mannanase of GH 113, Man113A, was identified in thermoacidophilic Alicyclobacillus sp. strain A4 and found to exhibit both hydrolytic and transglycosylation activities. The enzyme had a broad substrate spectrum, showed higher activities on glucomannan than on galactomannan, and released mannobiose and mannotriose as the main hydrolysis products after an extended incubation. Compared to the only functionally characterized and structure-resolved counterpart Alicyclobacillus acidocaldarius ManA (AaManA) of GH 113, Man113A showed much higher Catalytic efficiency on mannooligosaccharides, in the order mannohexaose ≈ mannopentaose > mannotetraose > mannotriose, and required at least four sugar units for efficient catalysis. Homology modeling, molecular docking analysis, and site-directed mutagenesis revealed the vital roles of eight residues (Trp13, Asn90, Trp96, Arg97, Tyr196, Trp274, Tyr292, and Cys143) related to substrate recognition by and Catalytic Mechanism of GH 113. Comparison of the binding pockets and key residues of β-mannanases of different families indicated that members of GH 113 and GH 5 have more residues serving as stacking platforms to support -4 to -1 subsites than those of GH 26 and that the residues preceding the acid/base catalyst are quite different. Taken as a whole, this study elucidates substrate recognition by and the Catalytic Mechanism of GH 113 β-mannanases and distinguishes them from counterparts of other families.

Bin Yao - One of the best experts on this subject based on the ideXlab platform.

  • A novel glycoside hydrolase family 113 endo-β-1,4-mannanase from Alicyclobacillus sp. strain A4 and insight into the substrate recognition and Catalytic Mechanism of this family
    Applied and Environmental Microbiology, 2016
    Co-Authors: Wei Xia, Haiqiang Lu, Mengjuan Xia, Lichun Qian, Pengjun Shi, Huiying Luo, Yingguo Bai, Ying Cui, Bin Yao
    Abstract:

    © 2016, American Society for Microbiology. All Rights Reserved.Few members of glycoside hydrolase (GH) family 113 have been characterized, and information on substrate recognition by and the Catalytic Mechanism of this family is extremely limited. In the present study, a novel endo-β-1,4-mannanase of GH 113, Man113A, was identified in thermoacidophilic Alicyclobacillus sp. strain A4 and found to exhibit both hydrolytic and transglycosylation activities. The enzyme had a broad substrate spectrum, showed higher activities on glucomannan than on galactomannan, and released mannobiose and mannotriose as the main hydrolysis products after an extended incubation. Compared to the only functionally characterized and structure-resolved counterpart Alicyclobacillus acidocaldarius ManA (AaManA) of GH 113, Man113A showed much higher Catalytic efficiency on mannooligosaccharides, in the order mannohexaose ≈ mannopentaose > mannotetraose > mannotriose, and required at least four sugar units for efficient catalysis. Homology modeling, molecular docking analysis, and site-directed mutagenesis revealed the vital roles of eight residues (Trp13, Asn90, Trp96, Arg97, Tyr196, Trp274, Tyr292, and Cys143) related to substrate recognition by and Catalytic Mechanism of GH 113. Comparison of the binding pockets and key residues of β-mannanases of different families indicated that members of GH 113 and GH 5 have more residues serving as stacking platforms to support -4 to -1 subsites than those of GH 26 and that the residues preceding the acid/base catalyst are quite different. Taken as a whole, this study elucidates substrate recognition by and the Catalytic Mechanism of GH 113 β-mannanases and distinguishes them from counterparts of other families.

Wei Xia - One of the best experts on this subject based on the ideXlab platform.

  • A novel glycoside hydrolase family 113 endo-β-1,4-mannanase from Alicyclobacillus sp. strain A4 and insight into the substrate recognition and Catalytic Mechanism of this family
    Applied and Environmental Microbiology, 2016
    Co-Authors: Wei Xia, Haiqiang Lu, Mengjuan Xia, Lichun Qian, Pengjun Shi, Huiying Luo, Yingguo Bai, Ying Cui, Bin Yao
    Abstract:

    © 2016, American Society for Microbiology. All Rights Reserved.Few members of glycoside hydrolase (GH) family 113 have been characterized, and information on substrate recognition by and the Catalytic Mechanism of this family is extremely limited. In the present study, a novel endo-β-1,4-mannanase of GH 113, Man113A, was identified in thermoacidophilic Alicyclobacillus sp. strain A4 and found to exhibit both hydrolytic and transglycosylation activities. The enzyme had a broad substrate spectrum, showed higher activities on glucomannan than on galactomannan, and released mannobiose and mannotriose as the main hydrolysis products after an extended incubation. Compared to the only functionally characterized and structure-resolved counterpart Alicyclobacillus acidocaldarius ManA (AaManA) of GH 113, Man113A showed much higher Catalytic efficiency on mannooligosaccharides, in the order mannohexaose ≈ mannopentaose > mannotetraose > mannotriose, and required at least four sugar units for efficient catalysis. Homology modeling, molecular docking analysis, and site-directed mutagenesis revealed the vital roles of eight residues (Trp13, Asn90, Trp96, Arg97, Tyr196, Trp274, Tyr292, and Cys143) related to substrate recognition by and Catalytic Mechanism of GH 113. Comparison of the binding pockets and key residues of β-mannanases of different families indicated that members of GH 113 and GH 5 have more residues serving as stacking platforms to support -4 to -1 subsites than those of GH 26 and that the residues preceding the acid/base catalyst are quite different. Taken as a whole, this study elucidates substrate recognition by and the Catalytic Mechanism of GH 113 β-mannanases and distinguishes them from counterparts of other families.