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Pre-Steady-State Kinetic Studies of Nucleotide Incorporation into a Single-Nucleotide Gapped DNA Substrate Catalyzed by Human DNA Polymerase β.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-11 DOI: 10.1021/acs.biochem.4c00804
Daniel Betancourt, Turner W Seay, Nikita Zalenski, Zucai Suo
{"title":"Pre-Steady-State Kinetic Studies of Nucleotide Incorporation into a Single-Nucleotide Gapped DNA Substrate Catalyzed by Human DNA Polymerase β.","authors":"Daniel Betancourt, Turner W Seay, Nikita Zalenski, Zucai Suo","doi":"10.1021/acs.biochem.4c00804","DOIUrl":"10.1021/acs.biochem.4c00804","url":null,"abstract":"<p><p>DNA polymerase β (Polβ) is a key enzyme in DNA base excision repair (BER). Despite extensive research, several microscopic rate constants within the kinetic mechanism of nucleotide incorporation into single-nucleotide gapped DNA by Polβ have not been determined and the identity of the rate-limiting step remains controversial. Here, we employed pre-steady-state kinetic methods and determined the rate constants for correct dNTP association (<i>k</i><sub>2</sub> = 4.5 × 10<sup>6</sup> M<sup>-1</sup> s<sup>-1</sup>) and dissociation (<i>k</i><sub><i>-</i>2</sub> = 118 s<sup>-1</sup>) as well as DNA product release (k<sub>7</sub>=0.93 s<sup>-1</sup>). Previously, uncertainty regarding the transition state of phosphodiester bond formation has led to confusion regarding the interpretation of the sulfur elemental effect between the incorporations of dNTP and its thio analog <i>S</i><sub>p</sub>-dNTPαS. However, recent results from time-resolved X-ray crystallographic studies of three DNA polymerases have allowed us to revise the benchmark of sulfur elemental effect for a rate-limiting chemistry step from 4-11 to 10-160. By using the revised benchmark, we determined the sulfur elemental effects for correct and incorrect nucleotide incorporation to be 3.94 and 64.6, respectively. These suggest the chemistry step limits mismatched, but not matched, nucleotide incorporation. Furthermore, the 2.1-fold difference in the reaction amplitudes of the pulse-quench and pulse-chase assays provides definitive evidence that a protein conformational change step prior to the chemistry step is rate-limiting for matched nucleotide incorporation. These findings unify the kinetic mechanism of correct nucleotide incorporation for Polβ and all other kinetically characterized DNA polymerases and reverse transcriptases, in which the protein conformational change prior to the chemistry step is rate-limiting.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1032-1041"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural Elucidation of the Reduced Mn(III)/Fe(III) Intermediate of the Radical-Initiating Metallocofactor in Chlamydia trachomatis Ribonucleotide Reductase.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-17 DOI: 10.1021/acs.biochem.4c00692
Ryan J Martinie, Jovan Livada, Nyaari Kothiya, J Martin Bollinger, Carsten Krebs, Alexey Silakov
{"title":"Structural Elucidation of the Reduced Mn(III)/Fe(III) Intermediate of the Radical-Initiating Metallocofactor in <i>Chlamydia trachomatis</i> Ribonucleotide Reductase.","authors":"Ryan J Martinie, Jovan Livada, Nyaari Kothiya, J Martin Bollinger, Carsten Krebs, Alexey Silakov","doi":"10.1021/acs.biochem.4c00692","DOIUrl":"10.1021/acs.biochem.4c00692","url":null,"abstract":"<p><p>Ribonucleotide reductases (RNRs) are the sole <i>de novo</i> source of deoxyribonucleotides for DNA synthesis and repair across all organisms and carry out their reaction via a radical mechanism. RNR from <i>Chlamydia trachomatis</i> generates its turnover-initiating cysteinyl radical by long-range reduction of a Mn(IV)/Fe(III) cofactor, producing a Mn(III)/Fe(III) intermediate. Herein, we characterize the protonation states of the inorganic ligands in this reduced state using advanced pulse electron paramagnetic resonance (EPR) spectroscopy and <sup>2</sup>H-isotope labeling. A strongly coupled deuteron is observed by hyperfine sublevel correlation (HYSCORE) spectroscopy experiments and indicates the presence of a bridging hydroxo ligand. Isotope-dependent EPR line broadening analysis and the magnitude of the estimated Mn-Fe exchange coupling constant together suggest a μ-oxo/μ-hydroxo core. Two distinct signals detected in electron-nuclear double resonance (ENDOR) spectra are attributable to less strongly coupled hydrons of a terminal water ligand to Mn(III). Together, these experiments imply that the reduced cofactor has a mixed μ-oxo/μ-hydroxo core with a terminal water ligand on Mn(III). This structural assignment sheds light generally on the reactivity of Mn/Fe heterobimetallic sites and, more specifically, on the proton-coupling in the electron transfer that initiates ribonucleotide reduction in this subclass of RNRs.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1157-1167"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein and DNA Conformational Changes Contribute to Specificity of Cre Recombinase. 蛋白质和DNA构象变化有助于提高Cre重组酶的特异性
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-16 DOI: 10.1021/acs.biochem.4c00841
Jonathan S Montgomery, Megan E Judson, Mark P Foster
{"title":"Protein and DNA Conformational Changes Contribute to Specificity of Cre Recombinase.","authors":"Jonathan S Montgomery, Megan E Judson, Mark P Foster","doi":"10.1021/acs.biochem.4c00841","DOIUrl":"10.1021/acs.biochem.4c00841","url":null,"abstract":"<p><p>Cre, a conservative site-specific tyrosine recombinase, is a powerful gene editing tool in the laboratory. Expanded applications in human health are hindered by a lack of understanding of the mechanism by which Cre selectively binds and recombines its cognate <i>loxP</i> sequences. This knowledge is essential for retargeting the enzyme to new sites and for mitigating the effects of off-target recombination. Prior studies have suggested that in addition to a few base-specific contacts to cognate <i>loxP</i> DNA, the enzyme's specificity is enhanced by (1) autoinhibition involving a conformational change in the protein's C-terminal helix and (2) indirect readout via binding-coupled conformational changes in the target DNA. We used isothermal titration calorimetry (ITC), circular dichroism (CD), and heteronuclear NMR spectroscopy to investigate DNA site recognition by wild-type Cre and a deletion mutant lacking the C-terminal helix. ITC of Cre and a C-terminal deletion variant against cognate and noncognate DNA recombinase binding elements (RBEs) reveal that the C-terminus reduces DNA binding affinity by 6-fold toward cognate DNA. Additionally, ITC revealed highly unfavorable binding enthalpy, which, when combined with evidence from CD and NMR of structural differences between cognate and noncognate complexes, supports a model in which binding-coupled DNA bending provides a unique structure-thermodynamic signature of cognate complexes. Together, these findings advance our understanding of site recognition by Cre recombinase.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1055-1064"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143431863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
From Negative to No Cooperativity: Effects of Mutations on Intersubunit Communication within F420H2:NADP+ Oxidoreductase Using Steady-State and Pre-Steady-State Kinetic Methods.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 DOI: 10.1021/acs.biochem.4c00416
Jamariya A Howard, Alaa Aziz, Lindsay A Davis, Denzel Pugh, Md Sabid Ahamed, Ravi Ramkissoon, Juan Corrales, Nathan T Nguyen, Charlene Mandimutsira, Tekleab Beyene, Co Ha, Calvin Dao, Parth Nikumbh, Adway O Zacharias, Saiful M Chowdhury, Kayunta Johnson-Winters
{"title":"From Negative to No Cooperativity: Effects of Mutations on Intersubunit Communication within F<sub>420</sub>H<sub>2</sub>:NADP<sup>+</sup> Oxidoreductase Using Steady-State and Pre-Steady-State Kinetic Methods.","authors":"Jamariya A Howard, Alaa Aziz, Lindsay A Davis, Denzel Pugh, Md Sabid Ahamed, Ravi Ramkissoon, Juan Corrales, Nathan T Nguyen, Charlene Mandimutsira, Tekleab Beyene, Co Ha, Calvin Dao, Parth Nikumbh, Adway O Zacharias, Saiful M Chowdhury, Kayunta Johnson-Winters","doi":"10.1021/acs.biochem.4c00416","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00416","url":null,"abstract":"<p><p>F<sub>420</sub>H<sub>2</sub>:NADP<sup>+</sup> oxidoreductase (Fno) catalyzes the reversible production of NADPH by transferring a hydride from the reduced F<sub>420</sub> cofactor to NADP<sup>+</sup>. Previous kinetic studies suggest that wild-type Fno (<i>wt</i>Fno) displays half-site reactivity and negative cooperativity, making Fno regulatory within methanogenic and sulfate-reducing archaea. These studies identified four amino acids; R186, T192, S190, and H133, as potential candidates involved in intersubunit communication due to their location either at or within close proximity to the interface of the dimer. Therefore, a library of Fno variants─R186K, R186Q, R186I, T192V, T192A, S190A, H133A, and H133N─was generated and characterized using binding, steady-state, and pre-steady-state kinetic experiments to understand their involvement in communication. The Hill coefficient for <i>wt</i>Fno was previously reported as 0.61 ± 0.03, while the R186K, R186Q, R186I, and T192V Fno variant values were close or equal to 1, indicating a switch to no cooperativity behavior. The S190A variant displayed increased Hill coefficients of 0.8 ± 0.1 when compared to <i>wt</i>Fno, showing that cooperativity was affected. The steady-state double reciprocal plots of the R186 variants, S190A, and T192V Fno variants were linear, which is indicative of no cooperativity, departing from the negative cooperativity shape displayed by <i>wt</i>Fno. Unlike <i>wt</i>Fno, the pre-steady-state kinetic experiments did not display half-site reactivity for the variants. Additionally, the hydride transfer step became rate-limiting in catalysis for the R186K Fno variant only. Our data suggest that negative cooperativity can be disrupted and that the amino acids R186, T192, and S190 are involved in intersubunit communication.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Inhibitors of SAMHD1 Obtained from Chemical Tethering to the Guanine Antiviral Acyclovir.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-24 DOI: 10.1021/acs.biochem.4c00854
Matthew Egleston, Shridhar Bhat, A Hasan Howlader, Mario A Bianchet, Yi Liu, Laura Maria Lopez Rovira, Brandon Smith, Marc M Greenberg, James T Stivers
{"title":"Inhibitors of SAMHD1 Obtained from Chemical Tethering to the Guanine Antiviral Acyclovir.","authors":"Matthew Egleston, Shridhar Bhat, A Hasan Howlader, Mario A Bianchet, Yi Liu, Laura Maria Lopez Rovira, Brandon Smith, Marc M Greenberg, James T Stivers","doi":"10.1021/acs.biochem.4c00854","DOIUrl":"10.1021/acs.biochem.4c00854","url":null,"abstract":"<p><p>Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is an enzyme with diverse activities. Its dNTPase activity degrades all canonical dNTPs and many anticancer nucleoside drugs, while its single-stranded nucleic acid binding activity promotes DNA repair and RNA homeostasis in cells. These functions require guanine nucleotide binding to a specific allosteric site (A1) on the enzyme. We previously described how the activities of SAMHD1 could be inhibited in vitro with fragment-based inhibitor design, using dGMP as a targeting fragment for the A1 site. However, these dGMP-tethered inhibitors had poor cell permeability due to the charged guanine monophosphate group. Here, we describe a new approach where the amino form of the guanine acyclic nucleoside acyclovir (NH<sub>2</sub>-ACV) is used as the targeting fragment, allowing facile coupling to activated carboxylic acids (R-COOH), either directly or using linkers. This approach generates a neutral amide instead of charged monophosphate attachment points. High-throughput screening of a ∼375 compound carboxylic acid library identified two compounds (<b>8</b>, <b>11</b>) with similar micromolar affinities for SAMHD1. Compound <b>11</b> was obtained by direct coupling to NH<sub>2</sub>-ACV, while compound <b>8</b> used a five-carbon linker. Both inhibitors had the same dibromonaphthol component from the carboxylic acid library screen. A crystal structure of a complex between SAMHD1 and <b>8,</b> combined with computational models of bound <b>11,</b> suggest how the dibromonaphthol promotes binding. The findings establish that guanine-based inhibitors targeting the A1 site do not require nucleotide or cyclic nucleoside structural elements. This guanine site targeting strategy is highly amenable to further chemical optimization.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1109-1120"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterization and Engineering of a Blue-Sensitive, Gi/o-Biased, and Bistable Ciliary Opsin from a Fan Worm.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-13 DOI: 10.1021/acs.biochem.4c00754
Sachiko Fukuzawa, Tomoki Kawaguchi, Takushi Shimomura, Yoshihiro Kubo, Hisao Tsukamoto
{"title":"Characterization and Engineering of a Blue-Sensitive, Gi/o-Biased, and Bistable Ciliary Opsin from a Fan Worm.","authors":"Sachiko Fukuzawa, Tomoki Kawaguchi, Takushi Shimomura, Yoshihiro Kubo, Hisao Tsukamoto","doi":"10.1021/acs.biochem.4c00754","DOIUrl":"10.1021/acs.biochem.4c00754","url":null,"abstract":"<p><p>Ciliary opsins (c-opsin) have been identified not only in vertebrates but also in invertebrates. An invertebrate ciliary opsin was recently identified in the fan worm <i>Acromegalomma interruptum</i> (formerly named <i>Megalomma interrupta</i>); however, its spectral and signaling characteristics are unknown. In the present study, we characterized the spectral properties and light-induced cellular signaling properties of opsin (<i>Acromegalomma</i> invertebrate ciliary opsin (<i>Acr</i>InvC-opsin)). <i>Acr</i>InvC-opsin showed an absorption maximum at 464 nm, and upon blue light absorption, the spectrum was red-shifted by approximately 50 nm. The two states are interconvertible by illumination with blue and orange light. Blue light illumination of <i>Acr</i>InvC-opsin caused specific coupling with Gi, sustained Gi dissociation, decreased intracellular cAMP levels, and the activation of GIRK channels. The cellular responses by the activated opsin were partially terminated by orange light illumination. These light-dependent responses indicate that InvC-opsin is a typical bistable pigment wherein the resting and activated states can be interconverted by visible light illumination. We also attempted to modulate the spectral and functional properties of <i>Acr</i>InvC-opsin by using site-directed mutagenesis. Substitution of Ser-94 with Ala caused little spectral shift in the resting state but a further red shift of ∼10 nm in the activated state, indicating that the absorption spectra of the two states were tuned differently. In contrast, the substitution of S94A did not significantly affect the light-dependent signaling properties of <i>Acr</i>InvC-opsin. Because <i>Acr</i>InvC-opsin is a blue-sensitive, Gi/o-biased, and bistable pigment, it has the potential to serve as an optical control tool to specifically and reversibly regulate Gi/o-dependent signaling pathways by visible light.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1020-1031"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-20 DOI: 10.1021/acs.biochem.4c00729
Niamh M Mockler, Kiefer O Ramberg, Ronan J Flood, Peter B Crowley
{"title":"N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor.","authors":"Niamh M Mockler, Kiefer O Ramberg, Ronan J Flood, Peter B Crowley","doi":"10.1021/acs.biochem.4c00729","DOIUrl":"10.1021/acs.biochem.4c00729","url":null,"abstract":"<p><p>We describe the capture and structuring of disordered N-terminal regions by the macrocycle sulfonato-calix[4]arene (<b>sclx</b><sub><b>4</b></sub>). Using the trimeric β-propeller <i>Ralstonia solanacearum</i> lectin (RSL) as a scaffold, we generated a series of mutants with extended and dynamic N-termini. Three of the mutants feature an N-terminal methionine-lysine motif. The fourth mutant contains the disordered 8-residue N-terminus of Histone 3, a component of the nucleosome. X-ray crystallography and NMR spectroscopy provide evidence for <b>sclx</b><sub><b>4</b></sub> binding to the flexible N-terminal regions. Three crystal structures reveal that the calixarene recognizes the N-terminal Met-Lys motif, capturing either residue. We provide crystallographic proof for <b>sclx</b><sub><b>4</b></sub> encapsulation of N-terminal methionine. Calixarene capture of intrinsically disordered regions may have applications in regulating protein secondary (and tertiary) structure.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1092-1098"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How Ligands Achieve Biased Signaling toward Arrestins.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-04 Epub Date: 2025-02-12 DOI: 10.1021/acs.biochem.4c00843
Qianru Jiang, Tao Che
{"title":"How Ligands Achieve Biased Signaling toward Arrestins.","authors":"Qianru Jiang, Tao Che","doi":"10.1021/acs.biochem.4c00843","DOIUrl":"10.1021/acs.biochem.4c00843","url":null,"abstract":"<p><p>G protein-coupled receptors (GPCRs) mediate the effects of various endogenous and extracellular stimuli through multiple transducers, including heterotrimeric G proteins, GPCR kinases (GRKs), and arrestins. Biased signaling, which preferentially activates certain G protein or GRK/arrestin signaling pathways, provides great opportunities for developing drugs with enhanced therapeutic efficacy and minimized side effects. In this Review, we review studies addressing the structural dynamics of GPCRs bound to balanced and biased ligands and current consensus on how ligand-receptor interactions determine signaling outcomes. We also examine the conformational changes in GPCRs when in complex with G proteins, arrestins, and GRKs, highlighting a more profound impact of signal transducers on receptor rearrangements compared with biased ligands. This evidence supports the idea that biased signaling can be achieved through the promotion of multiple conformational states by biased agonists and the stabilization of specific active conformations by individual signal transducers.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"967-977"},"PeriodicalIF":2.9,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143404893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Electrocatalytic Nitrite Reduction by a Monomeric NrfA: Commonality in Ammonification Mechanisms.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-03-03 DOI: 10.1021/acs.biochem.4c00761
Matt Tracy, Victor Sosa Alfaro, Julius Campeciño, Krystina Hird, Eric L Hegg, Nicolai Lehnert, Sean J Elliott
{"title":"Electrocatalytic Nitrite Reduction by a Monomeric NrfA: Commonality in Ammonification Mechanisms.","authors":"Matt Tracy, Victor Sosa Alfaro, Julius Campeciño, Krystina Hird, Eric L Hegg, Nicolai Lehnert, Sean J Elliott","doi":"10.1021/acs.biochem.4c00761","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00761","url":null,"abstract":"<p><p>Cytochrome <i>c</i> nitrite reductase (NrfA) is a pentaheme enzyme capable of the six-electron reduction of nitrite to ammonia, which is a key step in the nitrogen cycle. All NrfA enzymes appear to have a branched set of two heme-based pathways for electron transfer to a conserved active site, and until recently, NrfA enzymes from a variety of microorganisms were considered to possess a homodimeric structure; yet, recent efforts have shown that in solution, purified <i>Geobacter lovleyi</i> (<i>Gl</i>) NrfA is a monomer. Direct protein electrochemistry has been used in the past to characterize the dimeric NrfAs from <i>Escherichia coli</i> and <i>Shewanella oneidensis</i>, revealing features of maximal activity as a function of nitrite concentration, and redox poise, both of which were interpreted in terms of the dimeric structure providing multiple redox equivalents. Here, we examine <i>Gl</i> NrfA using protein film electrochemistry and find that all of the features that were associated with the dimeric enzymes are also found in the monomeric enzyme. Further, we probe the contribution of specific heme environments through investigation of two His to Met heme ligand mutants, each along a different branch of the electron transfer network, which demonstrates that each path is likely essential to support native-like catalysis.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and Characterization of the Two Glycosyltransferases Required for the Polymerization of the HS:1 Serotype Capsular Polysaccharide of Campylobacter jejuni G1.
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-02-28 DOI: 10.1021/acs.biochem.4c00803
Ronnie Bourland, Tamari Narindoshvili, Frank M Raushel
{"title":"Identification and Characterization of the Two Glycosyltransferases Required for the Polymerization of the HS:1 Serotype Capsular Polysaccharide of <i>Campylobacter jejuni</i> G1.","authors":"Ronnie Bourland, Tamari Narindoshvili, Frank M Raushel","doi":"10.1021/acs.biochem.4c00803","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00803","url":null,"abstract":"<p><p><i>Campylobacter jejuni</i> is a Gram-negative pathogenic bacterium commonly found in poultry and is the leading cause of gastrointestinal infections in the United States. Similar to other Gram-negative bacteria, <i>C. jejuni</i> possesses an extracellular carbohydrate-based capsular polysaccharide (CPS) composed of repeating units of monosaccharides bound via glycosidic linkages. The gene cluster for serotype 1 (HS:1) of <i>C. jejuni</i> contains 13 different genes required for the production and presentation of the CPS. Each repeating unit within the HS:1 CPS structure contains a backbone of glycerol phosphate and d-galactose. Here, the enzyme HS1.11 was shown to catalyze the formation of CDP-(2<i>R</i>)-glycerol from MgCTP and l-glycerol-3-phosphate. HS1.09 was found to be a multidomain protein that catalyzes the polymerization of l-glycerol-3-phosphate and d-galactose using UDP-d-galactose and CDP-(2<i>R</i>)-glycerol as substrates. The domain of HS1.09 that extends from residues 286 to 703 was shown to catalyze the transfer of l-glycerol-P from CDP-glycerol to the hydroxyl group at C4 of the d-galactose moiety at the nonreducing end of the growing oligosaccharide. The transfer of d-galactose to the C2 hydroxyl group of the glycerol-phosphate moiety was shown to be catalyzed with retention of configuration by the domain of HS1.09 that extends from residues 704 to 1095. Primers as short as a single d-galactoside were accepted as initial substrates. Oligosaccharide products were isolated by ion exchange chromatography and identified by high-resolution ESI-mass spectrometry and NMR spectroscopy.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143527812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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