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Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6. PLoS One 2020; 15:e0228708. [PMID: 32097412 PMCID: PMC7041794 DOI: 10.1371/journal.pone.0228708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/21/2020] [Indexed: 11/19/2022] Open
Abstract
The biomineralization protein Mms6 has been shown to be a major player in the formation of magnetic nanoparticles both within the magnetosomes of magnetotactic bacteria and as an additive in synthetic magnetite precipitation assays. Previous studies have highlighted the ferric iron binding capability of the protein and this activity is thought to be crucial to its mineralizing properties. To understand how this protein binds ferric ions we have prepared a series of single amino acid substitutions within the C-terminal binding region of Mms6 and have used a ferric binding assay to probe the binding site at the level of individual residues which has pinpointed the key residues of E44, E50 and R55 involved in Mms6 ferric binding. No aspartic residues bound ferric ions. A nanoplasmonic sensing experiment was used to investigate the unstable EER44, 50,55AAA triple mutant in comparison to native Mms6. This suggests a difference in interaction with iron ions between the two and potential changes to the surface precipitation of iron oxide when the pH is increased. All-atom simulations suggest that disruptive mutations do not fundamentally alter the conformational preferences of the ferric binding region. Instead, disruption of these residues appears to impede a sequence-specific motif in the C-terminus critical to ferric ion binding.
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2
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Doyle CM, Naser D, Bauman HA, Rumfeldt JA, Meiering EM. Spectrophotometric method for simultaneous measurement of zinc and copper in metalloproteins using 4-(2-pyridylazo)resorcinol. Anal Biochem 2019; 579:44-56. [DOI: 10.1016/j.ab.2019.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/04/2019] [Accepted: 03/17/2019] [Indexed: 12/26/2022]
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3
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Plieth C. Peroxide-Induced Liberation of Iron from Heme Switches Catalysis during Luminol Reaction and Causes Loss of Light and Heterodyning of Luminescence Kinetics. ACS OMEGA 2019; 4:3268-3279. [PMID: 31459543 PMCID: PMC6649120 DOI: 10.1021/acsomega.8b03564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/29/2019] [Indexed: 06/10/2023]
Abstract
The peroxidation of luminol yields bright luminescence when the reaction is catalyzed by heme proteins. However, an excess of peroxide leads to less light and altered luminescence kinetics, an effect commonly referred to as "suicide inactivation". The aim of this study is to present the molecular processes causing this effect. A comprehensive set of data reported here demonstrates that suicide inactivation is due to a peroxide-induced liberation of iron from its coordinating porphyrin. Liberated iron launches catalysis of the reaction at much lower efficiency. The light-yielding efficiencies of different organic and inorganic catalysts are precisely quantified and compared. It is shown that the catalysis by free iron involves superoxide. This is explained by the formation of a ferryl-oxo-iron complex. In this context, a complete reaction mechanism involving a modified Fenton-Haber-Weiss cycle is proposed for the first time. The switch from the highly efficient biogenically catalyzed luminescence to a less efficient inorganically catalyzed reaction is accompanied by a transition from "flash-type" to "glow-type" luminescence kinetics. Ethylenediaminetetraacetic acid-mediated chelation of iron is used to demonstrate this effect and to separate both kinetics. The explanation of kinetic heterodyning is underpinned by mathematical modeling. The results are able to explain the as yet unexplained phenomena discussed in the less recent literature and to settle disputes about them. It is concluded that peroxide concentrations exceeding the level tolerated by the catalyzing heme protein negatively impact performance and precision of luminol-based assays, where the light yield is used as a quantitative measure for analyte concentrations.
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Plieth C. Redox Modulators Determine Luminol Luminescence Generated by Porphyrin-Coordinated Iron and May Repress "Suicide Inactivation". ACS OMEGA 2018; 3:12295-12303. [PMID: 31459303 PMCID: PMC6645248 DOI: 10.1021/acsomega.8b01261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/14/2018] [Indexed: 05/29/2023]
Abstract
Iron porphyrin catalysts of the luminol reaction (horseradish peroxidase, hemoglobin, cytochrome c, and hemin) interact with diverse reducing compounds. Here, it is demonstrated how the chemiluminescence yield is modulated by such interactions. The compounds accepted as substrates protect the catalyst against the "suicide inactivation" caused by high peroxide concentrations. The reducing agents not accepted by the catalyst inhibit light production either by generating a futile redox cycle of the luminophore or by irreversibly inactivating the catalytic center. In the case of a futile cycle, light emission resumes as soon as the reducing agents in the reaction are consumed, whereas with an irreversible inactivation, light emission does not recover. The characteristics of luminescence enhancement and quenching depending on interfering agents are also reported here. They reveal details about the relative redox potentials of the involved compounds. It is discussed how this should be considered when the luminol reaction is used for quantitative analyses and when unpurified samples with a broad compound matrix are to be assayed.
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Affiliation(s)
- Christoph Plieth
- Zentrum für Biochemie und Molekularbiologie, Universität Kiel, Am Botanischen Garten 9, 24118 Kiel, Germany
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5
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Jha B, Kumar D, Sharma A, Dwivedy A, Singh R, Biswal BK. Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis. J Biol Chem 2018; 293:10102-10118. [PMID: 29752410 PMCID: PMC6028948 DOI: 10.1074/jbc.ra118.002299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/10/2018] [Indexed: 01/07/2023] Open
Abstract
The absence of a histidine biosynthesis pathway in humans, coupled with histidine essentiality for survival of the important human pathogen Mycobacterium tuberculosis (Mtb), underscores the importance of the bacterial enzymes of this pathway as major antituberculosis drug targets. However, the identity of the mycobacterial enzyme that functions as the histidinol phosphate phosphatase (HolPase) of this pathway remains to be established. Here, we demonstrate that the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate. The crystal structure of Rv3137 in apo form enabled us to dissect its distinct structural features. Furthermore, the holo-complex structure revealed that a unique cocatalytic multizinc-assisted mode of substrate binding and catalysis is the hallmark of Mtb HolPase. Interestingly, the enzyme-substrate complex structure unveiled that although monomers possess individual catalytic sites they share a common product-exit channel at the dimer interface. Furthermore, target-based screening against HolPase identified several small-molecule inhibitors of this enzyme. Taken together, our study unravels the missing enzyme link in the Mtb histidine biosynthesis pathway, augments our current mechanistic understanding of histidine production in Mtb, and has helped identify potential inhibitors of this bacterial pathway.
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Affiliation(s)
- Bhavya Jha
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Deepak Kumar
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Arun Sharma
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Abhisek Dwivedy
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Ramandeep Singh
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Bichitra Kumar Biswal
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and , Recipient of funding from the National Institute of Immunology, New Delhi, India. To whom correspondence should be addressed. Tel.:
91-11-26703705; Fax:
91-11-26742125; E-mail:
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6
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A family of metal-dependent phosphatases implicated in metabolite damage-control. Nat Chem Biol 2016; 12:621-7. [PMID: 27322068 DOI: 10.1038/nchembio.2108] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 03/30/2016] [Indexed: 12/31/2022]
Abstract
DUF89 family proteins occur widely in both prokaryotes and eukaryotes, but their functions are unknown. Here we define three DUF89 subfamilies (I, II, and III), with subfamily II being split into stand-alone proteins and proteins fused to pantothenate kinase (PanK). We demonstrated that DUF89 proteins have metal-dependent phosphatase activity against reactive phosphoesters or their damaged forms, notably sugar phosphates (subfamilies II and III), phosphopantetheine and its S-sulfonate or sulfonate (subfamily II-PanK fusions), and nucleotides (subfamily I). Genetic and comparative genomic data strongly associated DUF89 genes with phosphoester metabolism. The crystal structure of the yeast (Saccharomyces cerevisiae) subfamily III protein YMR027W revealed a novel phosphatase active site with fructose 6-phosphate and Mg(2+) bound near conserved signature residues Asp254 and Asn255 that are critical for activity. These findings indicate that DUF89 proteins are previously unrecognized hydrolases whose characteristic in vivo function is to limit potentially harmful buildups of normal or damaged phosphometabolites.
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8
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Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016; 283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
Abstract
7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Laura M Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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9
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Hagedoorn PL. Microbial Metalloproteomics. Proteomes 2015; 3:424-439. [PMID: 28248278 PMCID: PMC5217388 DOI: 10.3390/proteomes3040424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP)-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
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10
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Olson TL, Espiritu E, Edwardraja S, Simmons CR, Williams JC, Ghirlanda G, Allen JP. Design of dinuclear manganese cofactors for bacterial reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:539-547. [PMID: 26392146 DOI: 10.1016/j.bbabio.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
Abstract
A compelling target for the design of electron transfer proteins with novel cofactors is to create a model for the oxygen-evolving complex, a Mn4Ca cluster, of photosystem II. A mononuclear Mn cofactor can be added to the bacterial reaction center, but the addition of multiple metal centers is constrained by the native protein architecture. Alternatively, metal centers can be incorporated into artificial proteins. Designs for the addition of dinuclear metal centers to four-helix bundles resulted in three artificial proteins with ligands for one, two, or three dinuclear metal centers able to bind Mn. The three-dimensional structure determined by X-ray crystallography of one of the Mn-proteins confirmed the design features and revealed details concerning coordination of the Mn center. Electron transfer between these artificial Mn-proteins and bacterial reaction centers was investigated using optical spectroscopy. After formation of a light-induced, charge-separated state, the experiments showed that the Mn-proteins can donate an electron to the oxidized bacteriochlorophyll dimer of modified reaction centers, with the Mn-proteins having additional metal centers being more effective at this electron transfer reaction. Modeling of the structure of the Mn-protein docked to the reaction center showed that the artificial protein likely binds on the periplasmic surface similarly to cytochrome c2, the natural secondary donor. Combining reaction centers with exogenous artificial proteins provides the opportunity to create ligands and investigate the influence of inhomogeneous protein environments on multinuclear redox-active metal centers. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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11
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Fang C, Zhang L, Zhang X, Lu H. Selective enrichment of metal-binding proteins based on magnetic core/shell microspheres functionalized with metal cations. Analyst 2015; 140:4197-205. [PMID: 25913209 DOI: 10.1039/c5an00599j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Metal binding proteins play many important roles in a broad range of biological processes. Characterization of metal binding proteins is important for understanding their structure and biological functions, thus leading to a clear understanding of metal associated diseases. The present study is the first to investigate the effectiveness of magnetic microspheres functionalized with metal cations (Ca(2+), Cu(2+), Zn(2+) and Fe(3+)) as the absorbent matrix in IMAC technology to enrich metal containing/binding proteins. The putative metal binding proteins in rat liver were then globally characterized by using this strategy which is very easy to handle and can capture a number of metal binding proteins effectively. In total, 185 putative metal binding proteins were identified from rat liver including some known less abundant and membrane-bound metal binding proteins such as Plcg1, Acsl5, etc. The identified proteins are involved in many important processes including binding, catalytic activity, translation elongation factor activity, electron carrier activity, and so on.
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Affiliation(s)
- Caiyun Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
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12
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López-Castillo LM, López-Arciniega JAI, Guerrero-Rangel A, Valdés-Rodríguez S, Brieba LG, García-Lara S, Winkler R. Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect-resistant maize (Zea mays, p84C3) kernels by activity-directed purification. FRONTIERS IN PLANT SCIENCE 2015; 6:670. [PMID: 26379694 PMCID: PMC4553411 DOI: 10.3389/fpls.2015.00670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/13/2015] [Indexed: 05/03/2023]
Abstract
Plant peroxidases (PODs) are involved in diverse physiological processes, including defense against pathogens and insects. Contrary to their biological importance, only very few plant PODs have been proven on protein level, because their low abundance makes them difficult to detect in standard proteomics work-flows. A statistically significant positive correlation between POD activity and post-harvest insect resistance has been found for maize (Zea mays, p84C3) kernels. In combining activity-directed protein purification, genomic and proteomic tools we found that protein B6T173 (ZmPrx35) is responsible for the majority of the POD activity of the kernel. We successfully produced recombinant ZmPrx35 protein in Escherichia coli and demonstrate both, in vitro activity and the presence of a haem (heme) cofactor of the enzyme. Our findings support the screening for insect resistant maize variants and the construction of genetically optimized maize plants.
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Affiliation(s)
- Laura M. López-Castillo
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados – Instituto Politécnico NacionalIrapuato, Mexico
| | - Janet A. I. López-Arciniega
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
| | | | | | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados – Instituto Politécnico NacionalIrapuato, Mexico
| | | | - Robert Winkler
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
- *Correspondence: Robert Winkler, Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico,
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13
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Kushwaha AK, Deochand DK, Grove A. A moonlighting function of Mycobacterium smegmatis Ku in zinc homeostasis? Protein Sci 2014; 24:253-63. [PMID: 25450225 DOI: 10.1002/pro.2612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/25/2014] [Indexed: 01/14/2023]
Abstract
Ku protein participates in DNA double-strand break repair via the nonhomologous end-joining pathway. The three-dimensional structure of eukaryotic Ku reveals a central core consisting of a β-barrel domain and pillar and bridge regions that combine to form a ring-like structure that encircles DNA. Homologs of Ku are encoded by a subset of bacterial species, and they are predicted to conserve this core domain. In addition, the bridge region of Ku from some bacteria is predicted from homology modeling and sequence analyses to contain a conventional HxxC and CxxC (where x is any residue) zinc-binding motif. These potential zinc-binding sites have either deteriorated or been entirely lost in Ku from other organisms. Using an in vitro metal binding assay, we show that Mycobacterium smegmatis Ku binds two zinc ions. Zinc binding modestly stabilizes the Ku protein (by ∼3°C) and prevents cysteine oxidation, but it has little effect on DNA binding. In vivo, zinc induces significant upregulation of the gene encoding Ku (∼sixfold) as well as a divergently oriented gene encoding a predicted zinc-dependent MarR family transcription factor. Notably, overexpression of Ku confers zinc tolerance on Escherichia coli. We speculate that zinc-binding sites in Ku proteins from M. smegmatis and other mycobacterial species have been evolutionarily retained to provide protection against zinc toxicity without compromising the function of Ku in DNA double-strand break repair.
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Affiliation(s)
- Ambuj K Kushwaha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
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14
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Sherif M, Waung D, Korbeci B, Mavisakalyan V, Flick R, Brown G, Abou-Zaid M, Yakunin AF, Master ER. Biochemical studies of the multicopper oxidase (small laccase) from Streptomyces coelicolor using bioactive phytochemicals and site-directed mutagenesis. Microb Biotechnol 2013; 6:588-97. [PMID: 23815400 PMCID: PMC3918160 DOI: 10.1111/1751-7915.12068] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 11/30/2022] Open
Abstract
Multicopper oxidases can act on a broad spectrum of phenolic and non-phenolic compounds. These enzymes include laccases, which are widely distributed in plants and fungi, and were more recently identified in bacteria. Here, we present the results of biochemical and mutational studies of small laccase (SLAC), a multicopper oxidase from Streptomyces coelicolor (SCO6712). In addition to typical laccase substrates, SLAC was tested using phenolic compounds that exhibit antioxidant activity. SLAC showed oxidase activity against 12 of 23 substrates tested, including caffeic acid, ferulic acid, resveratrol, quercetin, morin, kaempferol and myricetin. The kinetic parameters of SLAC were determined for 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid), 2,6-dimethoxyphenol, quercetin, morin and myricetin, and maximum reaction rates were observed with myricetin, where kcat and Km values at 60°C were 8.1 (± 0.8) s−1 and 0.9 (± 0.3) mM respectively. SLAC had a broad pH optimum for activity (between pH 4 and 8) and temperature optimum at 60–70°C. It demonstrated remarkable thermostability with a half-life of over 10 h at 80°C and over 7 h at 90°C. Site-directed mutagenesis revealed 17 amino acid residues important for SLAC activity including the 10 His residues involved in copper coordination. Most notably, the Y229A and Y230A mutant proteins showed over 10-fold increase in activity compared with the wild-type SLAC, which was correlated to higher copper incorporation, while kinetic analyses with S929A predicts localization of this residue near the meta-position of aromatic substrates. Funding Information Funding for this research was provided by the Government of Ontario for the project ‘FFABnet: Functionalized Fibre and Biochemicals’ (ORF-RE-05-005), and the Natural Sciences and Engineering Research Council of Canada.
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Affiliation(s)
- Mohammed Sherif
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
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15
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Known and potential roles of transferrin in iron biology. Biometals 2012; 25:677-86. [PMID: 22294463 DOI: 10.1007/s10534-012-9520-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/06/2012] [Indexed: 12/13/2022]
Abstract
Transferrin is an abundant serum metal-binding protein best known for its role in iron delivery. The human disease congenital atransferrinemia and animal models of this disease highlight the essential role of transferrin in erythropoiesis and iron metabolism. Patients and mice deficient in transferrin exhibit anemia and a paradoxical iron overload attributed to deficiency in hepcidin, a peptide hormone synthesized largely by the liver that inhibits dietary iron absorption and macrophage iron efflux. Studies of inherited human disease and model organisms indicate that transferrin is an essential regulator of hepcidin expression. In this paper, we review current literature on transferrin deficiency and present our recent findings, including potential overlaps between transferrin, iron and manganese in the regulation of hepcidin expression.
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16
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Protein fractionation and detection for metalloproteomics: challenges and approaches. Anal Bioanal Chem 2012; 402:3311-22. [DOI: 10.1007/s00216-012-5743-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/09/2012] [Accepted: 01/12/2012] [Indexed: 12/17/2022]
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17
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Högbom M. Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclear—an intricate bioinorganic workaround to use different metals for the same reaction. Metallomics 2011; 3:110-20. [DOI: 10.1039/c0mt00095g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Miller JD, Sal MS, Schell M, Whittimore JD, Raulston JE. Chlamydia trachomatis YtgA is an iron-binding periplasmic protein induced by iron restriction. MICROBIOLOGY-SGM 2009; 155:2884-2894. [PMID: 19556290 DOI: 10.1099/mic.0.030247-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chlamydia trachomatis is a Gram-negative obligate intracellular bacterium that is the causative agent of common sexually transmitted diseases and the leading cause of preventable blindness worldwide. It has been observed that YtgA (CT067) is very immunogenic in patients with chlamydial genital infections. Homology analyses suggested that YtgA is a soluble periplasmic protein and a component of an ATP-binding cassette (ABC) transport system for metals such as iron. Since little is known about iron transport in C. trachomatis, biochemical assays were used to determine the potential role of YtgA in iron acquisition. (59)Fe binding and competition studies revealed that YtgA preferentially binds iron over nickel, zinc or manganese. Western blot and densitometry techniques showed that YtgA concentrations specifically increased 3-5-fold in C. trachomatis, when cultured under iron-starvation conditions rather than under general stress conditions, such as exposure to penicillin. Finally, immuno-transmission electron microscopy provided evidence that YtgA is more concentrated in C. trachomatis during iron restriction, supporting a possible role for YtgA as a component of an ABC transporter.
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Affiliation(s)
- J D Miller
- Dept of Molecular Biomedical Sciences, School of Veterinary Medicine, N.C. State University, Raleigh, NC 27606, USA
| | - M S Sal
- Dept of Microbiology, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 3761, USA
| | - M Schell
- Dept of Microbiology, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 3761, USA
| | - J D Whittimore
- Dept of Microbiology, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 3761, USA
| | - J E Raulston
- Dept of Pathology, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 3761, USA.,Dept of Microbiology, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 3761, USA
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19
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Andersson CS, Högbom M. A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold. Proc Natl Acad Sci U S A 2009; 106:5633-8. [PMID: 19321420 PMCID: PMC2667070 DOI: 10.1073/pnas.0812971106] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Indexed: 11/18/2022] Open
Abstract
Chlamydia trachomatis R2c is the prototype for a recently discovered group of ribonucleotide reductase R2 proteins that use a heterodinuclear Mn/Fe redox cofactor for radical generation and storage. Here, we show that the Mycobacterium tuberculosis protein Rv0233, an R2 homologue and a potential virulence factor, contains the heterodinuclear manganese/iron-carboxylate cofactor but displays a drastic remodeling of the R2 protein scaffold into a ligand-binding oxidase. The first structural characterization of the heterodinuclear cofactor shows that the site is highly specific for manganese and iron in their respective positions despite a symmetric arrangement of coordinating residues. In this protein scaffold, the Mn/Fe cofactor supports potent 2-electron oxidations as revealed by an unprecedented tyrosine-valine crosslink in the active site. This wolf in sheep's clothing defines a distinct functional group among R2 homologues and may represent a structural and functional counterpart of the evolutionary ancestor of R2s and bacterial multicomponent monooxygenases.
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Affiliation(s)
- Charlotta S. Andersson
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences C4, SE-106 91 Stockholm, Sweden; and
| | - Martin Högbom
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences C4, SE-106 91 Stockholm, Sweden; and
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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20
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Development of a generic approach to native metalloproteomics: application to the quantitative identification of soluble copper proteins in Escherichia coli. J Biol Inorg Chem 2009; 14:631-40. [DOI: 10.1007/s00775-009-0477-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 01/24/2009] [Indexed: 10/21/2022]
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21
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Yeeles JTP, Cammack R, Dillingham MS. An iron-sulfur cluster is essential for the binding of broken DNA by AddAB-type helicase-nucleases. J Biol Chem 2009; 284:7746-55. [PMID: 19129187 DOI: 10.1074/jbc.m808526200] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial helicase-nuclease complex AddAB converts double-stranded DNA breaks into substrates for RecA-dependent recombinational repair. Here we show that the AddB subunit contains a novel class of nuclease domain distinguished by the presence of an iron-sulfur cluster. The cluster is coordinated by an unusual arrangement of cysteine residues that originate from both sides of the AddB nuclease, forming an "iron staple" that is required for the local structural integrity of this domain. Disruption of the iron-sulfur cluster by mutagenesis eliminates the ability of AddAB to bind to duplex DNA ends without affecting the single-stranded DNA-dependent ATPase activity. Sequence analysis suggests that a related iron staple nuclease domain is present in the eukaryotic DNA replication/repair factor Dna2, where it is also associated with a DNA helicase motor.
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Affiliation(s)
- Joseph T P Yeeles
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
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22
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Bogel G, Schrempf H, Ortiz de Orué Lucana D. The heme-binding protein HbpS regulates the activity of the Streptomyces reticuli iron-sensing histidine kinase SenS in a redox-dependent manner. Amino Acids 2008; 37:681-91. [PMID: 18931968 DOI: 10.1007/s00726-008-0188-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 10/01/2008] [Indexed: 12/18/2022]
Abstract
The SenS/SenR system of Streptomyces reticuli regulates the expression of the redox regulator FurS, the catalase-peroxidase CpeB and the heme-binding protein HbpS. SenS/SenR is also proposed to participate in sensing redox changes, mediated by HbpS. Here, we show in vitro that heme-free HbpS represses the autokinase activity of SenS; whereas hemin-treated HbpS considerably enhances SenS autophosphorylation under redox conditions using either H(2)O(2) or DTT. The presence of iron ions alone or in combination with H(2)O(2) or DTT also leads to significantly increased phosphorylation levels of SenS. Further comparative physiological studies using the S. reticuli WT, a S. reticuli hbpS mutant and a S. reticuli senS-senR mutant corroborates the importance of HbpS and the SenS/SenR system for resistance against high concentrations of iron ions and hemin in vivo. Hence SenS/SenR and HbpS act in concert as a novel three-component system which detects redox stress, mediated by iron ions and heme.
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Affiliation(s)
- Gabriele Bogel
- FB Biologie/Chemie, Angewandte Genetik der Mikroorganismen, Universität Osnabrück, Barbarastr. 13, 49069, Osnabrück, Germany
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23
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Abstract
Transition metals are among the most common ligands that contribute to the biochemical and physiological properties of proteins. In the course of structural proteomic projects, the detection of transition metal cofactors prior to the determination of a high-resolution structure is extremely beneficial. This information can be used to select tractable targets from the proteomic pipeline because the presence of a metal often improves protein stability and can be used to help solve the phasing problem in x-ray crystallography. Recombinant proteins are often purified with substoichiometric amounts of metal loaded, so additional metal may be needed to obtain the homogeneous protein solution crucial for structural analysis. Furthermore, identifying a metal cofactor provides a clue about the nature of the biological role of an unclassified protein and can be applied with structural data in the assignation of a putative function. Many of the existing methods for transition metal analysis of purified proteins have limitations, which include a requirement for a large quantity of protein or a reliance on equipment with a prohibitive cost.The authors have developed two simple high throughput methods for identifying metalloproteins on a microgram scale. Each of the techniques has distinct advantages and can be applied to address divergent experimental goals. The first method, based on simple luminescence and colorimetric reactions, is fast, cheap, and semiquantitative. The second method, which employs HPLC separation, is accurate and affords unambiguous metal identification.
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24
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Bertini I, Cavallaro G. Metals in the “omics” world: copper homeostasis and cytochrome c oxidase assembly in a new light. J Biol Inorg Chem 2007; 13:3-14. [DOI: 10.1007/s00775-007-0316-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 10/25/2007] [Indexed: 01/20/2023]
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25
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Proudfoot M, Sanders SA, Singer A, Zhang R, Brown G, Binkowski A, Xu L, Lukin JA, Murzin AG, Joachimiak A, Arrowsmith CH, Edwards AM, Savchenko AV, Yakunin AF. Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain. J Mol Biol 2007; 375:301-15. [PMID: 18021800 DOI: 10.1016/j.jmb.2007.10.060] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 10/23/2007] [Accepted: 10/24/2007] [Indexed: 12/22/2022]
Abstract
We have identified a novel family of proteins, in which the N-terminal cystathionine beta-synthase (CBS) domain is fused to the C-terminal Zn ribbon domain. Four proteins were overexpressed in Escherichia coli and purified: TA0289 from Thermoplasma acidophilum, TV1335 from Thermoplasma volcanium, PF1953 from Pyrococcus furiosus, and PH0267 from Pyrococcus horikoshii. The purified proteins had a red/purple color in solution and an absorption spectrum typical of rubredoxins (Rds). Metal analysis of purified proteins revealed the presence of several metals, with iron and zinc being the most abundant metals (2-67% of iron and 12-74% of zinc). Crystal structures of both mercury- and iron-bound TA0289 (1.5-2.0 A resolution) revealed a dimeric protein whose intersubunit contacts are formed exclusively by the alpha-helices of two cystathionine beta-synthase subdomains, whereas the C-terminal domain has a classical Zn ribbon planar architecture. All proteins were reversibly reduced by chemical reductants (ascorbate or dithionite) or by the general Rd reductase NorW from E. coli in the presence of NADH. Reduced TA0289 was found to be capable of transferring electrons to cytochrome C from horse heart. Likewise, the purified Zn ribbon protein KTI11 from Saccharomyces cerevisiae had a purple color in solution and an Rd-like absorption spectrum, contained both iron and zinc, and was reduced by the Rd reductase NorW from E. coli. Thus, recombinant Zn ribbon domains from archaea and yeast demonstrate an Rd-like electron carrier activity in vitro. We suggest that, in vivo, some Zn ribbon domains might also bind iron and therefore possess an electron carrier activity, adding another physiological role to this large family of important proteins.
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Affiliation(s)
- Michael Proudfoot
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Room 72, Toronto, ON, Canada
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26
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
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27
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Andreini C, Banci L, Bertini I, Elmi S, Rosato A. Non-heme iron through the three domains of life. Proteins 2007; 67:317-24. [PMID: 17286284 DOI: 10.1002/prot.21324] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Metalloproteins are proteins capable of binding one or more metal ions, which are often required for their biological function or for regulation of their activities or for structural purposes. In high-throughput genome-level protein investigation efforts, such as Structural Genomics, the systematic experimental characterization of metal-binding properties (i.e. the investigation of the metalloproteome) is not always pursued, and remains far from trivial. In the present work we have applied a bioinformatic approach to investigate the occurrence of (putative) non-heme iron-binding proteins in 57 different organisms spanning the entire tree of life. It is found that the non-heme iron-proteome constitutes between 1% and 10% of the entire proteome of an organism. However, the iron-proteome constitutes a higher fraction of the proteome in archaea (on average 7.1% +/- 2.1%) than in bacteria (3.9% +/- 1.6%) and in eukaryota (1.1% +/- 0.4%). The analysis of the function of each putative iron-protein identified suggests that extant organisms have inherited the large majority of their iron-proteome from the last common ancestor.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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28
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Passerini A, Andreini C, Menchetti S, Rosato A, Frasconi P. Predicting zinc binding at the proteome level. BMC Bioinformatics 2007; 8:39. [PMID: 17280606 PMCID: PMC1800866 DOI: 10.1186/1471-2105-8-39] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 02/05/2007] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial. RESULTS The present work reports on the development of a machine learning method for the prediction of the zinc-binding state of pairs of nearby amino-acids, using predictors based on support vector machines. The predictor was trained using chains containing zinc-binding sites and non-metalloproteins in order to provide positive and negative examples. Results based on strong non-redundancy tests prove that (1) zinc-binding residues can be predicted and (2) modelling the correlation between the binding state of nearby residues significantly improves performance. The trained predictor was then applied to the human proteome. The present results were in good agreement with the outcomes of previous, highly manually curated, efforts for the identification of human zinc-binding proteins. Some unprecedented zinc-binding sites could be identified, and were further validated through structural modelling. The software implementing the predictor is freely available at: http://zincfinder.dsi.unifi.it CONCLUSION The proposed approach constitutes a highly automated tool for the identification of metalloproteins, which provides results of comparable quality with respect to highly manually refined predictions. The ability to model correlations between pairwise residues allows it to obtain a significant improvement over standard 1D based approaches. In addition, the method permits the identification of unprecedented metal sites, providing important hints for the work of experimentalists.
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Affiliation(s)
- Andrea Passerini
- Machine Learning and Neural Networks Group, Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Italy
| | - Claudia Andreini
- Magnetic Resonance Center (CERM) and Dipartimento di Chimica, Università degli Studi di Firenze, Italy
| | - Sauro Menchetti
- Machine Learning and Neural Networks Group, Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Dipartimento di Chimica, Università degli Studi di Firenze, Italy
| | - Paolo Frasconi
- Machine Learning and Neural Networks Group, Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Italy
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29
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Abstract
Zinc is one of the metal ions essential for life, as it is required for the proper functioning of a large number of proteins. Despite its importance, the annotation of zinc-binding proteins in gene banks or protein domain databases still has significant room for improvement. In the present work, we compiled a list of known zinc-binding protein domains and of known zinc-binding sequence motifs (zinc-binding patterns), and then used them jointly to analyze the proteome of 57 different organisms to obtain an overview of zinc usage by archaeal, bacterial, and eukaryotic organisms. Zinc-binding proteins are an abundant fraction of these proteomes, ranging between 4% and 10%. The number of zinc-binding proteins correlates linearly with the total number of proteins encoded by the genome of an organism, but the proportionality constant of Eukaryota (8.8%) is significantly higher than that observed in Bacteria and Archaea (from 5% to 6%). Most of this enrichment is due to the larger portfolio of regulatory proteins in Eukaryota.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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30
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Ferrer M, Golyshina OV, Beloqui A, Golyshin PN, Timmis KN. The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 2007; 445:91-4. [PMID: 17203061 DOI: 10.1038/nature05362] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 10/20/2006] [Indexed: 11/09/2022]
Abstract
Ferroplasma is a genus of the Archaea, one of the three branches of the tree of life, and belongs to the order Thermoplasmatales (Euryarchaeota), which contains the most acidophilic microbes yet known. Ferroplasma species live in acid mine drainage, acidic pools and environments containing sulphidic ores such as pyrite and characterized by pH values of 0-2 and high concentrations of ferrous iron and other heavy metals. F. acidiphilum strain Y(T) is a chemoautotroph that grows optimally at pH 1.7 and gains energy by oxidizing ferrous iron and carbon by the fixation of carbon dioxide. Here we show that 86% of 189 investigated cellular proteins of F. acidiphilum are iron-metalloproteins. These include proteins with deduced structural, chaperone and catalytic roles, not described as iron-metalloproteins in any other organism so far investigated. The iron atoms in the proteins seem to organize and stabilize their three-dimensional structures, to act as 'iron rivets'. Analysis of proteins of the phylogenetic neighbour Picrophilus torridus and of the habitat neighbour Acidithiobacillus ferrooxidans revealed far fewer and only typical metalloproteins. F. acidiphilum therefore has a currently unique iron-protein-dominated cellular machinery and biochemical phylogeny.
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Affiliation(s)
- Manuel Ferrer
- CSIC, Institute of Catalysis, Cantoblanco, 28049 Madrid, Spain.
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31
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Andreini C, Banci L, Bertini I, Rosato A. Counting the zinc-proteins encoded in the human genome. J Proteome Res 2006; 5:196-201. [PMID: 16396512 DOI: 10.1021/pr050361j] [Citation(s) in RCA: 702] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, or for regulation of their activities or for structural purposes. Genome sequencing projects have provided a huge number of protein primary sequences, but, even though several different elaborate analyses and annotations have been enabled by a rich and ever-increasing portfolio of bioinformatic tools, metal-binding properties remain difficult to predict as well as to investigate experimentally. Consequently, the present knowledge about metalloproteins is only partial. The present bioinformatic research proposes a strategy to answer the question of how many and which proteins encoded in the human genome may require zinc for their physiological function. This is achieved by a combination of approaches, which include: (i) searching in the proteome for the zinc-binding patterns that, on their turn, are obtained from all available X-ray data; (ii) using libraries of metal-binding protein domains based on multiple sequence alignments of known metalloproteins obtained from the Pfam database; and (iii) mining the annotations of human gene sequences, which are based on any type of information available. It is found that 1684 proteins in the human proteome are independently identified by all three approaches as zinc-proteins, 746 are identified by two, and 777 are identified by only one method. By assuming that all proteins identified by at least two approaches are truly zinc-binding and inspecting the proteins identified by a single method, it can be proposed that ca. 2800 human proteins are potentially zinc-binding in vivo, corresponding to 10% of the human proteome, with an uncertainty of 400 sequences. Available functional information suggests that the large majority of human zinc-binding proteins are involved in the regulation of gene expression. The most abundant class of zinc-binding proteins in humans is that of zinc-fingers, with Cys4 and Cys2His2 being the most common types of coordination environment.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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