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  1. Article ; Online: Expanding the viewpoint: Leveraging sequence information in enzymology.

    Knox, Hayley L / Allen, Karen N

    Current opinion in chemical biology

    2023  Volume 72, Page(s) 102246

    Abstract: The use of protein sequence to inform enzymology in terms of structure, mechanism, and function has burgeoned over the past two decades. Referred to as genomic enzymology, the utilization of bioinformatic tools such as sequence similarity networks and ... ...

    Abstract The use of protein sequence to inform enzymology in terms of structure, mechanism, and function has burgeoned over the past two decades. Referred to as genomic enzymology, the utilization of bioinformatic tools such as sequence similarity networks and phylogenetic analyses has allowed the identification of new substrates and metabolites, novel pathways, and unexpected reaction mechanisms. The holistic examination of superfamilies can yield insight into the origins and paths of evolution of enzymes and the range of their substrates and mechanisms. Herein, we highlight advances in the use of genomic enzymology to address problems which the in-depth analyses of a single enzyme alone could not enable.
    MeSH term(s) Phylogeny ; Genomics ; Computational Biology ; Enzymes/metabolism
    Chemical Substances Enzymes
    Language English
    Publishing date 2023-01-02
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/j.cbpa.2022.102246
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  2. Article ; Online: Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA.

    Vuksanovic, Nemanja / Clasman, Jozlyn R / Imperiali, Barbara / Allen, Karen N

    Protein science : a publication of the Protein Society

    2024  Volume 33, Issue 1, Page(s) e4848

    Abstract: In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans ... ...

    Abstract In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N-acetylgalatosamine (GalNAc) from uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) to undecaprenyl-diphospho-N,N'-diacetylbacillosamine (UndPP-diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane-embedded acceptor and the structural analysis of the complex together with bioinformatics and site-directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″-OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate-specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
    MeSH term(s) Glycosyltransferases/chemistry ; Campylobacter/metabolism ; Polysaccharides/metabolism ; Sugars ; Substrate Specificity
    Chemical Substances Glycosyltransferases (EC 2.4.-) ; Polysaccharides ; Sugars
    Language English
    Publishing date 2024-01-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4848
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  3. Article ; Online: MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability.

    Muellers, Samantha N / Allen, Karen N / Whitty, Adrian

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 49, Page(s) e2309884120

    Abstract: Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal ... ...

    Abstract Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal stability based on comparison of the amino acid sequences of homologous proteins derived from bacteria that grow at different temperatures. A key feature of the method is that it compares the sequences based not simply on the amino acid identity, but rather on the structural and physicochemical properties of the side chain. The method accurately identified stabilizing substitutions in three well-studied systems and was validated prospectively by experimentally testing predicted stabilizing substitutions in a polyamine oxidase. In each case, the method outperformed the widely used bioinformatic consensus approach. The method can also provide insight into fundamental aspects of protein structure, for example, by identifying how many sequence positions in a given protein are relevant to temperature adaptation.
    MeSH term(s) Protein Stability ; Amino Acid Sequence ; Mutation ; Proteins/genetics ; Machine Learning ; Enzyme Stability
    Chemical Substances Mentat ; Proteins
    Language English
    Publishing date 2023-12-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2309884120
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  4. Article ; Online: Preface.

    Allen, Karen N

    Methods in enzymology

    2018  Volume 607, Page(s) xv–xviii

    MeSH term(s) Computer Simulation ; Enzyme Assays/instrumentation ; Enzyme Assays/methods ; Models, Molecular ; Phosphoric Monoester Hydrolases/chemistry ; Phosphoric Monoester Hydrolases/metabolism ; Protein Conformation ; Substrate Specificity
    Chemical Substances Phosphoric Monoester Hydrolases (EC 3.1.3.2)
    Language English
    Publishing date 2018-06-30
    Publishing country United States
    Document type Editorial ; Introductory Journal Article
    ISSN 1557-7988 ; 0076-6879
    ISSN (online) 1557-7988
    ISSN 0076-6879
    DOI 10.1016/S0076-6879(18)30315-X
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  5. Article ; Online: The Birth of Genomic Enzymology: Discovery of the Mechanistically Diverse Enolase Superfamily.

    Allen, Karen N / Whitman, Christian P

    Biochemistry

    2021  Volume 60, Issue 46, Page(s) 3515–3528

    Abstract: Enzymes are categorized into superfamilies by sequence, structural, and mechanistic similarities. The evolutionary implications can be profound. Until the mid-1990s, the approach was fragmented largely due to limited sequence and structural data. However, ...

    Abstract Enzymes are categorized into superfamilies by sequence, structural, and mechanistic similarities. The evolutionary implications can be profound. Until the mid-1990s, the approach was fragmented largely due to limited sequence and structural data. However, in 1996, Babbitt et al. published a paper in
    MeSH term(s) Biochemistry/history ; Biochemistry/methods ; Evolution, Molecular ; Genomics/history ; Genomics/methods ; History, 20th Century ; Phosphopyruvate Hydratase/genetics ; Phosphopyruvate Hydratase/history ; Phosphopyruvate Hydratase/metabolism ; Sequence Homology, Amino Acid
    Chemical Substances Phosphopyruvate Hydratase (EC 4.2.1.11)
    Language English
    Publishing date 2021-10-19
    Publishing country United States
    Document type Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.1c00494
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    Zs.A 217: Show issues Location:
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  6. Article ; Online: Co-conserved sequence motifs are predictive of substrate specificity in a family of monotopic phosphoglycosyl transferases.

    Anderson, Alyssa J / Dodge, Greg J / Allen, Karen N / Imperiali, Barbara

    Protein science : a publication of the Protein Society

    2023  Volume 32, Issue 6, Page(s) e4646

    Abstract: Monotopic phosphoglycosyl transferases (monoPGTs) are an expansive superfamily of enzymes that catalyze the first membrane-committed step in the biosynthesis of bacterial glycoconjugates. MonoPGTs show a strong preference for their cognate nucleotide ... ...

    Abstract Monotopic phosphoglycosyl transferases (monoPGTs) are an expansive superfamily of enzymes that catalyze the first membrane-committed step in the biosynthesis of bacterial glycoconjugates. MonoPGTs show a strong preference for their cognate nucleotide diphospho-sugar (NDP-sugar) substrates. However, despite extensive characterization of the monoPGT superfamily through previous development of a sequence similarity network comprising >38,000 nonredundant sequences, the connection between monoPGT sequence and NDP-sugar substrate specificity has remained elusive. In this work, we structurally characterize the C-terminus of a prototypic monoPGT for the first time and show that 19 C-terminal residues play a significant structural role in a subset of monoPGTs. This new structural information facilitated the identification of co-conserved sequence "fingerprints" that predict NDP-sugar substrate specificity for this subset of monoPGTs. A Hidden Markov model was generated that correctly assigned the substrate of previously unannotated monoPGTs. Together, these structural, sequence, and biochemical analyses have delivered new insight into the determinants guiding substrate specificity of monoPGTs and have provided a strategy for assigning the NDP-sugar substrate of a subset of enzymes in the superfamily that use UDP-di-N-acetyl bacillosamine. Moving forward, this approach may be applied to identify additional sequence motifs that serve as fingerprints for monoPGTs of differing UDP-sugar substrate specificity.
    MeSH term(s) Transferases/chemistry ; Substrate Specificity ; Conserved Sequence ; Sugars ; Uridine Diphosphate
    Chemical Substances Transferases (EC 2.-) ; Sugars ; Uridine Diphosphate (58-98-0)
    Language English
    Publishing date 2023-04-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4646
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  7. Book: Phosphatases

    Allen, Karen N

    (Methods in enzymology ; volume 607)

    2018  

    Author's details edited by Karen N. Allen, Department of Chemistry, Boston University, Boston, MA, United States
    Series title Methods in enzymology ; volume 607
    Language English
    Size xviii, 422 Seiten, Illustrationen, Diagramme
    Edition First edition
    Document type Book
    ISBN 9780128138816 ; 0128138815
    Database Leibniz Institute of Plant Genetics and Crop Plant Research

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  8. Article ; Online: Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity.

    Tararina, Margarita A / Allen, Karen N

    Journal of molecular biology

    2020  Volume 432, Issue 10, Page(s) 3269–3288

    Abstract: The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant sequences represented in all domains of life. Of the thousands of members identified, only 214 have been functionally annotated to date, and 40 unique structures are ... ...

    Abstract The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant sequences represented in all domains of life. Of the thousands of members identified, only 214 have been functionally annotated to date, and 40 unique structures are represented in the Protein Data Bank. The few functionally characterized members share a catalytic mechanism involving the oxidation of an amine substrate through transfer of a hydride to the FAD cofactor, with differences observed in substrate specificities. Previous studies have focused on comparing a subset of superfamily members. Here, we present a comprehensive analysis of the FAO superfamily based on reaction mechanism and substrate recognition. Using a dataset of 9192 sequences, a sequence similarity network, and subsequently, a genome neighborhood network were constructed, organizing the superfamily into eight subgroups that accord with substrate type. Likewise, through phylogenetic analysis, the evolutionary relationship of subgroups was determined, delineating the divergence between enzymes based on organism, substrate, and mechanism. In addition, using sequences and atomic coordinates of 22 structures from the Protein Data Bank to perform sequence and structural alignments, active-site elements were identified, showing divergence from the canonical aromatic-cage residues to accommodate large substrates. These specificity determinants are held in a structural framework comprising a core domain catalyzing the oxidation of amines with an auxiliary domain for substrate recognition. Overall, analysis of the FAO superfamily reveals a modular fold with cofactor and substrate-binding domains allowing for diversity of recognition via insertion/deletions. This flexibility allows facile evolution of new activities, as shown by reinvention of function between subfamilies.
    MeSH term(s) Amino Acid Sequence ; Catalytic Domain ; Dinitrocresols/chemistry ; Dinitrocresols/metabolism ; Evolution, Molecular ; Models, Molecular ; Monoamine Oxidase/chemistry ; Monoamine Oxidase/genetics ; Monoamine Oxidase/metabolism ; Multigene Family ; Phylogeny ; Protein Conformation ; Sequence Alignment ; Substrate Specificity
    Chemical Substances Dinitrocresols ; 4,6-dinitro-o-cresol (1604ZJR09T) ; Monoamine Oxidase (EC 1.4.3.4)
    Language English
    Publishing date 2020-03-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.03.007
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  9. Article ; Online: Structural and mechanistic themes in glycoconjugate biosynthesis at membrane interfaces.

    Allen, Karen N / Imperiali, Barbara

    Current opinion in structural biology

    2019  Volume 59, Page(s) 81–90

    Abstract: Peripheral and integral membrane proteins feature in stepwise assembly of complex glycans and glycoconjugates. Catalysis on membrane-bound substrates features challenges with substrate solubility and active-site accessibility. However, advantages in ... ...

    Abstract Peripheral and integral membrane proteins feature in stepwise assembly of complex glycans and glycoconjugates. Catalysis on membrane-bound substrates features challenges with substrate solubility and active-site accessibility. However, advantages in enzyme and substrate orientation and control of lateral membrane diffusion provide order to the multistep processes. Recent glycosyltransferase (GT) studies show that substrate diversity is met by the selection of folds which do not converge upon a common mechanism. Examples of polyprenol phosphate phosphoglycosyl transferases (PGTs) highlight that divergent fold families catalyze the same reaction with different mechanisms. Lipid A biosynthesis enzymes illustrate that variations on the robust Rossmann fold allow substrate diversity. Improved understanding of GT and PGT structure and function holds promise for better function prediction and improvement of therapeutic inhibitory ligands.
    MeSH term(s) Binding Sites ; Carbohydrate Metabolism ; Catalysis ; Catalytic Domain ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cellulose/chemistry ; Cellulose/metabolism ; Glucosyltransferases/chemistry ; Glucosyltransferases/metabolism ; Glycoconjugates/biosynthesis ; Glycoconjugates/chemistry ; Glycosyltransferases/chemistry ; Glycosyltransferases/metabolism ; Lipid A/biosynthesis ; Lipid A/chemistry ; Polyprenols/chemistry ; Polyprenols/metabolism ; Polysaccharides/chemistry ; Quantitative Structure-Activity Relationship ; Substrate Specificity
    Chemical Substances Glycoconjugates ; Lipid A ; Polyprenols ; Polysaccharides ; Cellulose (9004-34-6) ; Glycosyltransferases (EC 2.4.-) ; Glucosyltransferases (EC 2.4.1.-) ; cellulose synthase (EC 2.4.1.-)
    Language English
    Publishing date 2019-04-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2019.03.013
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  10. Article ; Online: Glycoconjugate pathway connections revealed by sequence similarity network analysis of the monotopic phosphoglycosyl transferases.

    O'Toole, Katherine H / Imperiali, Barbara / Allen, Karen N

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 4

    Abstract: The monotopic phosphoglycosyl transferase (monoPGT) superfamily comprises over 38,000 nonredundant sequences represented in bacterial and archaeal domains of life. Members of the superfamily catalyze the first membrane-committed step in en bloc ... ...

    Abstract The monotopic phosphoglycosyl transferase (monoPGT) superfamily comprises over 38,000 nonredundant sequences represented in bacterial and archaeal domains of life. Members of the superfamily catalyze the first membrane-committed step in en bloc oligosaccharide biosynthetic pathways, transferring a phosphosugar from a soluble nucleoside diphosphosugar to a membrane-resident polyprenol phosphate. The singularity of the monoPGT fold and its employment in the pivotal first membrane-committed step allows confident assignment of both protein and corresponding pathway. The diversity of the family is revealed by the generation and analysis of a sequence similarity network for the superfamily, with fusion of monoPGTs with other pathway members being the most frequent and extensive elaboration. Three common fusions were identified: sugar-modifying enzymes, glycosyl transferases, and regulatory domains. Additionally, unexpected fusions of the monoPGT with members of the polytopic PGT superfamily were discovered, implying a possible evolutionary link through the shared polyprenol phosphate substrate. Notably, a phylogenetic reconstruction of the monoPGT superfamily shows a radial burst of functionalization, with a minority of members comprising only the minimal PGT catalytic domain. The commonality and identity of the fusion partners in the monoPGT superfamily is consistent with advantageous colocalization of pathway members at membrane interfaces.
    MeSH term(s) Amino Acid Sequence ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Binding Sites ; Cytoplasm/enzymology ; Cytoplasm/genetics ; Evolution, Molecular ; Gene Expression ; Gene Regulatory Networks ; Glycoconjugates/chemistry ; Glycoconjugates/metabolism ; Glycosyltransferases/chemistry ; Glycosyltransferases/genetics ; Glycosyltransferases/metabolism ; Gram-Negative Bacteria/classification ; Gram-Negative Bacteria/enzymology ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/classification ; Gram-Positive Bacteria/enzymology ; Gram-Positive Bacteria/genetics ; Metabolic Networks and Pathways/genetics ; Models, Molecular ; Periplasm/enzymology ; Periplasm/genetics ; Phylogeny ; Polysaccharides/chemistry ; Polysaccharides/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity
    Chemical Substances Bacterial Proteins ; Glycoconjugates ; Polysaccharides ; Glycosyltransferases (EC 2.4.-)
    Language English
    Publishing date 2021-01-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2018289118
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