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  1. Article ; Online: From the Three-Dimensional Structure of Phosphotriesterase.

    Holden, Hazel M / Raushel, Frank M

    Biochemistry

    2021  Volume 60, Issue 46, Page(s) 3413–3415

    MeSH term(s) Catalytic Domain ; Crystallography, X-Ray/history ; History, 20th Century ; Humans ; Nerve Agents/metabolism ; Organophosphates/metabolism ; Phosphoric Triester Hydrolases/metabolism ; Phosphoric Triester Hydrolases/ultrastructure ; Protein Multimerization ; Protein Structure, Quaternary ; Structure-Activity Relationship
    Chemical Substances Nerve Agents ; Organophosphates ; Phosphoric Triester Hydrolases (EC 3.1.8.-)
    Language English
    Publishing date 2021-06-03
    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.1c00311
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  2. Article ; Online: Biosynthesis of Cytidine Diphosphate-6-d-Glucitol for the Capsular Polysaccharides of

    Ghosh, Manas K / Narindoshvili, Tamari / Thoden, James B / Schumann, Mitchell E / Holden, Hazel M / Raushel, Frank M

    Biochemistry

    2024  Volume 63, Issue 5, Page(s) 699–710

    Abstract: Campylobacter ... ...

    Abstract Campylobacter jejuni
    MeSH term(s) Animals ; Humans ; Campylobacter jejuni ; Sorbitol/metabolism ; Chickens/metabolism ; Polysaccharides/metabolism ; Cytidine Diphosphate/metabolism ; Fructose/metabolism ; Polysaccharides, Bacterial/metabolism
    Chemical Substances Sorbitol (506T60A25R) ; Polysaccharides ; Cytidine Diphosphate (63-38-7) ; Fructose (30237-26-4) ; Polysaccharides, Bacterial
    Language English
    Publishing date 2024-02-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00706
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  3. Article ; Online: Structure and function of an N-acetyltransferase from the human pathogen Acinetobacter baumannii isolate BAL_212.

    Herkert, Noah R / Thoden, James B / Holden, Hazel M

    Proteins

    2022  Volume 90, Issue 8, Page(s) 1594–1605

    Abstract: Acinetobacter baumannii is a Gram-negative bacterium commonly found in soil and water that can cause human infections of the blood, lungs, and urinary tract. Of particular concern is its prevalence in health-care settings where it can survive on surfaces ...

    Abstract Acinetobacter baumannii is a Gram-negative bacterium commonly found in soil and water that can cause human infections of the blood, lungs, and urinary tract. Of particular concern is its prevalence in health-care settings where it can survive on surfaces and shared equipment for extended periods of time. The capsular polysaccharide surrounding the organism is known to be the major contributor to virulence. The structure of the K57 capsular polysaccharide produced by A. baumannii isolate BAL_212 from Vietnam was recently shown to contain the rare sugar 4-acetamido-4,6-dideoxy-d-glucose. Three enzymes are required for its biosynthesis, one of which is encoded by the gene H6W49_RS17300 and referred to as VioB, a putative N-acetyltransferase. Here, we describe a combined structural and functional analysis of VioB. Kinetic analyses show that the enzyme does, indeed, function on dTDP-4-amino-4,6-dideoxy-d-glucose with a catalytic efficiency of 3.9 x 10
    MeSH term(s) Acetyltransferases/chemistry ; Acinetobacter baumannii/genetics ; Acinetobacter baumannii/metabolism ; Catalysis ; Humans ; Kinetics ; Sugars
    Chemical Substances Sugars ; Acetyltransferases (EC 2.3.1.-)
    Language English
    Publishing date 2022-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.26334
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  4. Article ; Online: Editorial overview: Catalysis and regulation: Structural features guiding enzyme catalysed processes.

    Vrielink, Alice / Holden, Hazel M

    Current opinion in structural biology

    2018  Volume 53, Page(s) iii–v

    MeSH term(s) Biocatalysis ; Enzymes/chemistry
    Chemical Substances Enzymes
    Language English
    Publishing date 2018-10-16
    Publishing country England
    Document type Editorial
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2018.11.008
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  5. Article ; Online: Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar.

    Linehan, Michael P / Thoden, James B / Holden, Hazel M

    The Journal of biological chemistry

    2021  Volume 296, Page(s) 100463

    Abstract: Psychrobacter cryohalolentis strain ... ...

    Abstract Psychrobacter cryohalolentis strain K5
    MeSH term(s) Acetyl Coenzyme A/chemistry ; Acetyl Coenzyme A/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biosynthetic Pathways ; Catalytic Domain ; Crystallography, X-Ray/methods ; Galactose/metabolism ; Kinetics ; Lipopolysaccharides/chemistry ; Monosaccharides/biosynthesis ; Monosaccharides/chemistry ; Protein Conformation ; Psychrobacter/enzymology ; Psychrobacter/genetics ; Psychrobacter/metabolism ; Sugars/metabolism ; Transaminases ; Uridine Diphosphate N-Acetylglucosamine/metabolism
    Chemical Substances 2,4-diacetamido-2,4,6-trideoxy-D-glucose ; Bacterial Proteins ; Lipopolysaccharides ; Monosaccharides ; Sugars ; Uridine Diphosphate N-Acetylglucosamine (528-04-1) ; Acetyl Coenzyme A (72-89-9) ; Transaminases (EC 2.6.1.-) ; Galactose (X2RN3Q8DNE)
    Language English
    Publishing date 2021-02-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2021.100463
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  6. Article ; Online: C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from

    Ghosh, Manas K / Xiang, Dao Feng / Thoden, James B / Holden, Hazel M / Raushel, Frank M

    Biochemistry

    2022  Volume 61, Issue 18, Page(s) 2036–2048

    Abstract: Campylobacter ... ...

    Abstract Campylobacter jejuni
    MeSH term(s) Amino Acids/metabolism ; Campylobacter jejuni ; Hydro-Lyases/metabolism ; Oxidoreductases/metabolism ; Polysaccharides/metabolism ; Racemases and Epimerases/metabolism
    Chemical Substances Amino Acids ; Polysaccharides ; Oxidoreductases (EC 1.-) ; Hydro-Lyases (EC 4.2.1.-) ; Racemases and Epimerases (EC 5.1.-)
    Language English
    Publishing date 2022-09-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.2c00364
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  7. Article ; Online: Reaction Mechanism and Three-Dimensional Structure of GDP-d-glycero-α-d-manno-heptose 4,6-Dehydratase from

    Xiang, Dao Feng / Thoden, James B / Ghosh, Manas K / Holden, Hazel M / Raushel, Frank M

    Biochemistry

    2022  Volume 61, Issue 13, Page(s) 1313–1322

    Abstract: Campylobacter ... ...

    Abstract Campylobacter jejuni
    MeSH term(s) Bacterial Proteins/chemistry ; Campylobacter jejuni ; Heptoses/chemistry ; Humans ; Hydro-Lyases/metabolism ; Protons ; Water/metabolism
    Chemical Substances Bacterial Proteins ; Heptoses ; Protons ; Water (059QF0KO0R) ; Hydro-Lyases (EC 4.2.1.-)
    Language English
    Publishing date 2022-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.2c00244
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  8. Article ; Online: Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.

    Thoden, James B / McKnight, James O / Kroft, Charles W / Jast, Joshua D T / Holden, Hazel M

    The Journal of biological chemistry

    2023  Volume 299, Issue 10, Page(s) 105200

    Abstract: The sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, was first identified ∼40 years ago in the O-antigen of Pseudomonas aeruginosa O:3,a,d. Since then, it has been observed on the O-antigens of various pathogenic Gram-negative bacteria including ... ...

    Abstract The sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, was first identified ∼40 years ago in the O-antigen of Pseudomonas aeruginosa O:3,a,d. Since then, it has been observed on the O-antigens of various pathogenic Gram-negative bacteria including Bordetella pertussis, Escherichia albertii, and Pseudomonas mediterranea. Previous studies have established that five enzymes are required for its biosynthesis beginning with uridine dinucleotide (UDP)-N-acetyl-d-glucosamine (UDP-GlcNAc). The final step in the pathway is catalyzed by a 2-epimerase, which utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate. Curious as to whether this biochemical pathway is found in extreme thermophiles, we examined the published genome sequence for Thermus thermophilus HB27 and identified five ORFs that could possibly encode for the required enzymes. The focus of this investigation is on the ORF WP_011172736, which we demonstrate encodes for a 2-epimerase. For this investigation, ten high resolution X-ray crystallographic structures were determined to resolutions of 2.3 Å or higher. The models have revealed the manner in which the 2-epimerase anchors its UDP-sugar substrate as well as its UDP-sugar product into the active site. In addition, this study reveals for the first time the manner in which any sugar 2-epimerase can simultaneously bind UDP-sugars in both the active site and the allosteric binding region. We have also demonstrated that the T. thermophilus enzyme is allosterically regulated by UDP-GlcNAc. Whereas the sugar 2-epimerases that function on UDP-GlcNAc have been the focus of past biochemical and structural analyses, this is the first detailed investigation of a 2-epimerase that specifically utilizes UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid as its substrate.
    MeSH term(s) Carbohydrate Epimerases/chemistry ; Catalytic Domain ; O Antigens ; Racemases and Epimerases/metabolism ; Sugars ; Uridine Diphosphate Sugars ; Thermus thermophilus/enzymology ; Biocatalysis
    Chemical Substances 2,3-diacetamido-2,3-dideoxy-glucuronic acid (79319-92-9) ; Carbohydrate Epimerases (EC 5.1.3.-) ; O Antigens ; Racemases and Epimerases (EC 5.1.-) ; Sugars ; Uridine Diphosphate Sugars
    Language English
    Publishing date 2023-09-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.105200
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  9. Article ; Online: Investigation of the enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-glucuronic acid in Psychrobacter cryohalolentis K5

    Hofmeister, Daniel L / Seltzner, Chase A / Bockhaus, Nicholas J / Thoden, James B / Holden, Hazel M

    Protein science : a publication of the Protein Society

    2022  Volume 32, Issue 1, Page(s) e4502

    Abstract: Psychrobacter cryohalolentis ... ...

    Abstract Psychrobacter cryohalolentis K5
    MeSH term(s) Glucuronic Acid ; Oxidoreductases ; Uridine Diphosphate ; Acetyltransferases/chemistry ; Transaminases ; Sugars
    Chemical Substances 2,3-diacetamido-2,3-dideoxy-glucuronic acid (79319-92-9) ; Glucuronic Acid (8A5D83Q4RW) ; Oxidoreductases (EC 1.-) ; Uridine Diphosphate (58-98-0) ; Acetyltransferases (EC 2.3.1.-) ; Transaminases (EC 2.6.1.-) ; Sugars
    Language English
    Publishing date 2022-11-08
    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.4502
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  10. Article ; Online: Characterization of a novel inhibitor for the New Delhi metallo-β-lactamase-4: Implications for drug design and combating bacterial drug resistance.

    Thoden, James B / Benin, Bogdan M / Priebe, Adam / Shin, Woo Shik / Muthyala, Ramaiah / Sham, Yuk Yin / Holden, Hazel M

    The Journal of biological chemistry

    2023  Volume 299, Issue 9, Page(s) 105135

    Abstract: The bacterial metallo-β-lactamases (MBLs) catalyze the inactivation of β-lactam antibiotics. Identifying novel pharmacophores remains crucial for the clinical development of additional MBL inhibitors. Previously, 1-hydroxypyridine-2(1H)-thione-6- ... ...

    Abstract The bacterial metallo-β-lactamases (MBLs) catalyze the inactivation of β-lactam antibiotics. Identifying novel pharmacophores remains crucial for the clinical development of additional MBL inhibitors. Previously, 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid, hereafter referred to as 1,2-HPT-6-COOH, was reported as a low cytotoxic nanomolar β-lactamase inhibitor of Verona-integron-encoded metallo-β-lactamase 2, capable of rescuing β-lactam antibiotic activity. In this study, we explore its exact mechanism of inhibition and the extent of its activity through structural characterization of its binding to New Delhi metallo-β-lactamase 4 (NDM-4) and its inhibitory activity against both NDM-1 and NDM-4. Of all the structure-validated MBL inhibitors available, 1,2-HPT-6-COOH is the first discovered compound capable of forming an octahedral coordination sphere with Zn2 of the binuclear metal center. This unexpected mechanism of action provides important insight for the further optimization of 1,2-HPT-6-COOH and the identification of additional pharmacophores for MBL inhibition.
    Language English
    Publishing date 2023-08-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.105135
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