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  1. Article ; Online: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase.

    Mullins, Elwood A / Salay, Lauren E / Durie, Clarissa L / Bradley, Noah P / Jackman, Jane E / Ohi, Melanie D / Chazin, Walter J / Eichman, Brandt F

    Nature structural & molecular biology

    2024  

    Abstract: The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis ... ...

    Abstract The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-024-01227-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase.

    Cordoba, John J / Mullins, Elwood A / Salay, Lauren E / Eichman, Brandt F / Chazin, Walter J

    Journal of molecular biology

    2023  Volume 435, Issue 24, Page(s) 168330

    Abstract: DNA replication in eukaryotes relies on the synthesis of a ∼30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C- ... ...

    Abstract DNA replication in eukaryotes relies on the synthesis of a ∼30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ∼20 nucleotides of DNA. Here, we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the surprisingly low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
    MeSH term(s) Humans ; DNA Primase/metabolism ; DNA Primers ; DNA Replication ; RNA/metabolism
    Chemical Substances DNA polymerase alpha-primase (EC 2.7.7.-) ; DNA Primase (EC 2.7.7.-) ; DNA Primers ; PRIM1 protein, human (EC 2.7.7.-) ; RNA (63231-63-0) ; RNA primers
    Language English
    Publishing date 2023-10-24
    Publishing country Netherlands
    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.2023.168330
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase.

    Cordoba, John J / Mullins, Elwood A / Salay, Lauren E / Eichman, Brandt F / Chazin, Walter J

    bioRxiv : the preprint server for biology

    2023  

    Abstract: DNA replication in eukaryotes relies on the synthesis of a ~30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C- ... ...

    Abstract DNA replication in eukaryotes relies on the synthesis of a ~30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ~20 nucleotides of DNA. Here we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
    Language English
    Publishing date 2023-08-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.01.551538
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase.

    Mullins, Elwood A / Salay, Lauren E / Durie, Clarissa L / Bradley, Noah P / Jackman, Jane E / Ohi, Melanie D / Chazin, Walter J / Eichman, Brandt F

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in ... ...

    Abstract The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
    Language English
    Publishing date 2023-09-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.16.533013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites.

    Mullins, Elwood A / Dorival, Jonathan / Tang, Gong-Li / Boger, Dale L / Eichman, Brandt F

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 6942

    Abstract: Microbes produce a broad spectrum of antibiotic natural products, including many DNA-damaging genotoxins. Among the most potent of these are DNA alkylating agents in the spirocyclopropylcyclohexadienone (SCPCHD) family, which includes the duocarmycins, ... ...

    Abstract Microbes produce a broad spectrum of antibiotic natural products, including many DNA-damaging genotoxins. Among the most potent of these are DNA alkylating agents in the spirocyclopropylcyclohexadienone (SCPCHD) family, which includes the duocarmycins, CC-1065, gilvusmycin, and yatakemycin. The yatakemycin biosynthesis cluster in Streptomyces sp. TP-A0356 contains an AlkD-related DNA glycosylase, YtkR2, that serves as a self-resistance mechanism against yatakemycin toxicity. We previously reported that AlkD, which is not present in an SCPCHD producer, provides only limited resistance against yatakemycin. We now show that YtkR2 and C10R5, a previously uncharacterized homolog found in the CC-1065 biosynthetic gene cluster of Streptomyces zelensis, confer far greater resistance against their respective SCPCHD natural products. We identify a structural basis for substrate specificity across gene clusters and show a correlation between in vivo resistance and in vitro enzymatic activity indicating that reduced product affinity-not enhanced substrate recognition-is the evolutionary outcome of selective pressure to provide self-resistance against yatakemycin and CC-1065.
    MeSH term(s) Anti-Bacterial Agents/metabolism ; Bacterial Proteins/metabolism ; DNA Damage ; DNA Glycosylases/metabolism ; DNA Repair ; Duocarmycins/metabolism ; Multigene Family ; Mutagens/metabolism ; Streptomyces/genetics ; Streptomyces/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Duocarmycins ; Mutagens ; yatakemycin ; DNA Glycosylases (EC 3.2.2.-)
    Language English
    Publishing date 2021-11-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-27284-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway.

    Mullins, Elwood A / Rodriguez, Alyssa A / Bradley, Noah P / Eichman, Brandt F

    Trends in biochemical sciences

    2019  Volume 44, Issue 9, Page(s) 765–781

    Abstract: The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome ... ...

    Abstract The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome maintenance and metabolism, including sequence-specific restriction modification and repair of bulky adducts and interstrand crosslinks. Central to this expanded biological utility are specialized DNA glycosylases - enzymes that selectively excise damaged, modified, or mismatched nucleobases. In this review we discuss the newly identified roles of the BER pathway and examine the structural and mechanistic features of the DNA glycosylases that enable these functions.
    MeSH term(s) DNA/chemistry ; DNA/metabolism ; DNA Damage ; DNA Glycosylases/chemistry ; DNA Glycosylases/metabolism ; DNA Repair ; Humans
    Chemical Substances DNA (9007-49-2) ; DNA Glycosylases (EC 3.2.2.-)
    Language English
    Publishing date 2019-05-09
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2019.04.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Toxicity and repair of DNA adducts produced by the natural product yatakemycin.

    Mullins, Elwood A / Shi, Rongxin / Eichman, Brandt F

    Nature chemical biology

    2017  Volume 13, Issue 9, Page(s) 1002–1008

    Abstract: Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin family of natural products. Though bulky DNA lesions the size of those ... ...

    Abstract Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin family of natural products. Though bulky DNA lesions the size of those produced by YTM are normally removed from the genome by the nucleotide-excision repair (NER) pathway, YTM adducts are also a substrate for the bacterial DNA glycosylases AlkD and YtkR2, unexpectedly implicating base-excision repair (BER) in their elimination. The reason for the extreme toxicity of these lesions and the molecular basis for the way they are eliminated by BER have been unclear. Here, we describe the structural and biochemical properties of YTM adducts that are responsible for their toxicity, and define the mechanism by which they are excised by AlkD. These findings delineate an alternative strategy for repair of bulky DNA damage and establish the cellular utility of this pathway relative to that of NER.
    MeSH term(s) Biological Products/pharmacology ; Biological Products/toxicity ; DNA Adducts/drug effects ; DNA Damage ; DNA Repair/drug effects ; Drug Resistance, Bacterial ; Indoles/pharmacology ; Indoles/toxicity ; Molecular Structure ; Pyrroles/pharmacology ; Pyrroles/toxicity
    Chemical Substances Biological Products ; DNA Adducts ; Indoles ; Pyrroles ; yatakemycin
    Language English
    Publishing date 2017-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/nchembio.2439
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway

    Mullins, Elwood A / Rodriguez, Alyssa A / Bradley, Noah P / Eichman, Brandt F

    Trends in biochemical sciences. 2019 Sept., v. 44, no. 9

    2019  

    Abstract: The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome ... ...

    Abstract The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome maintenance and metabolism, including sequence-specific restriction modification and repair of bulky adducts and interstrand crosslinks. Central to this expanded biological utility are specialized DNA glycosylases – enzymes that selectively excise damaged, modified, or mismatched nucleobases. In this review we discuss the newly identified roles of the BER pathway and examine the structural and mechanistic features of the DNA glycosylases that enable these functions.
    Keywords DNA ; DNA repair ; crosslinking ; genome ; glycosylases ; metabolism ; nucleobases
    Language English
    Dates of publication 2019-09
    Size p. 765-781.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2019.04.006
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase.

    Murphy, Jesse R / Mullins, Elwood A / Kappock, T Joseph

    Frontiers in chemistry

    2016  Volume 4, Page(s) 23

    Abstract: Coenzyme A (CoA)-transferases catalyze the reversible transfer of CoA from acyl-CoA thioesters to free carboxylates. Class I CoA-transferases produce acylglutamyl anhydride intermediates that undergo attack by CoA thiolate on either the internal or ... ...

    Abstract Coenzyme A (CoA)-transferases catalyze the reversible transfer of CoA from acyl-CoA thioesters to free carboxylates. Class I CoA-transferases produce acylglutamyl anhydride intermediates that undergo attack by CoA thiolate on either the internal or external carbonyl carbon atoms, forming distinct tetrahedral intermediates <3 Å apart. In this study, crystal structures of succinyl-CoA:acetate CoA-transferase (AarC) from Acetobacter aceti are used to examine how the Asn347 carboxamide stabilizes the internal oxyanion intermediate. A structure of the active mutant AarC-N347A bound to CoA revealed both solvent replacement of the missing contact and displacement of the adjacent Glu294, indicating that Asn347 both polarizes and orients the essential glutamate. AarC was crystallized with the nonhydrolyzable acetyl-CoA (AcCoA) analog dethiaacetyl-CoA (1a) in an attempt to trap a closed enzyme complex containing a stable analog of the external oxyanion intermediate. One active site contained an acetylglutamyl anhydride adduct and truncated 1a, an unexpected result hinting at an unprecedented cleavage of the ketone moiety in 1a. Solution studies confirmed that 1a decomposition is accompanied by production of near-stoichiometric acetate, in a process that seems to depend on microbial contamination but not AarC. A crystal structure of AarC bound to the postulated 1a truncation product (2a) showed complete closure of one active site per dimer but no acetylglutamyl anhydride, even with acetate added. These findings suggest that an activated acetyl donor forms during 1a decomposition; a working hypothesis involving ketone oxidation is offered. The ability of 2a to induce full active site closure furthermore suggests that it subverts a system used to impede inappropriate active site closure on unacylated CoA.
    Language English
    Publishing date 2016-05-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2016.00023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Crystal structures of Acetobacter aceti succinyl-coenzyme A (CoA):acetate CoA-transferase reveal specificity determinants and illustrate the mechanism used by class I CoA-transferases.

    Mullins, Elwood A / Kappock, T Joseph

    Biochemistry

    2012  Volume 51, Issue 42, Page(s) 8422–8434

    Abstract: Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested ... ...

    Abstract Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested that acyl-CoA binding energy is used to accelerate rate-limiting acyl transfers by compressing the substrate thioester tightly against the catalytic glutamate [White, H., and Jencks, W. P. (1976) J. Biol. Chem. 251, 1688-1699]. The class I CoA-transferase succinyl-CoA:acetate CoA-transferase is an acetic acid resistance factor (AarC) with a role in a variant citric acid cycle in Acetobacter aceti. In an effort to identify residues involved in substrate recognition, X-ray crystal structures of a C-terminally His(6)-tagged form (AarCH6) were determined for several wild-type and mutant complexes, including freeze-trapped acetylglutamyl anhydride and glutamyl-CoA thioester adducts. The latter shows the acetate product bound to an auxiliary site that is required for efficient carboxylate substrate recognition. A mutant in which the catalytic glutamate was changed to an alanine crystallized in a closed complex containing dethiaacetyl-CoA, which adopts an unusual curled conformation. A model of the acetyl-CoA Michaelis complex demonstrates the compression anticipated four decades ago by Jencks and reveals that the nucleophilic glutamate is held at a near-ideal angle for attack as the thioester oxygen is forced into an oxyanion hole composed of Gly388 NH and CoA N2″. CoA is nearly immobile along its entire length during all stages of the enzyme reaction. Spatial and sequence conservation of key residues indicates that this mechanism is general among class I CoA-transferases.
    MeSH term(s) Acetobacter/enzymology ; Acyl Coenzyme A/metabolism ; Coenzyme A-Transferases/chemistry ; Coenzyme A-Transferases/metabolism ; Crystallography, X-Ray ; Models, Molecular
    Chemical Substances Acyl Coenzyme A ; succinyl-coenzyme A (BSI27HW5EQ) ; Coenzyme A-Transferases (EC 2.8.3.-) ; acetate-succinate CoA-transferase (EC 2.8.3.-)
    Language English
    Publishing date 2012-10-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/bi300957f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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