Crystal structure of a novel non‐Pfam protein AF1514 from <i>Archeoglobus fulgidus</i> DSM 4304 solved by S‐SAD using a Cr X‐ray source

Li, Yang; Bahti, Pazilat; Shaw, Neil; Song, Gaojie; Chen, Shunmei; Zhang, Xuejun; Zhang, Min; Cheng, Chu Yong; Yin, Jie; Zhu, Jin; Zhang, Hua; Che, Dongsheng; Xu, Hao; Abbas, Abdulla; Wang, Bi Cheng; Liu, Zhi Jie

doi:10.1002/prot.22025

Cited by 8 publications

(7 citation statements)

References 30 publications

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“…Another possible method to consider is halide soaking (or cocrystallization), in which new anomalous scatterers such as bromide and iodide are introduced to replace water or chloride. Both methods have proved to be effective in previous studies (Dauter et al, 2000;Yang et al, 2003;Xu et al, 2005;Watanabe et al, 2005;Yogavel et al, 2007;Li et al, 2008). Here, in our structural study of the protein BsDegV, the anomalous dispersion of sulfurs was quite weak and bromide incorpora-tion was inefficient.…”

Section: Discussionmentioning

confidence: 63%

“…In addition to the sulfurs from cysteine and methionine residues and sulfate ions, there are often other atoms that can potentially be used in SAD phasing, such as the P atom in phosphate, Cl atoms from buffers and (for example) the calcium, magnesium, iron and zinc metal ions present in many metalloproteins. Also, with the introduction of in-house chromium radiation sources, the anomalous scattering factor f of sulfur is doubled at the Cr K wavelength of 2.29 Å compared with the Cu K wavelength (1.54 Å ; Yang et al, 2003;Xu et al, 2005;Watanabe et al, 2005;Li et al, 2008). Indeed, most of these atoms have a significant increase (twofold) in anomalous scattering using Cr radiation.…”

Section: Introductionmentioning

confidence: 99%

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Structure of a fatty acid-binding protein fromBacillus subtilisdetermined by sulfur-SAD phasing using in-house chromium radiation

Nan

Zhou

Yang

et al. 2009

Acta Crystallogr D Biol Cryst

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Sulfur single-wavelength anomalous dispersion (S-SAD) and halide-soaking methods are increasingly being used for ab initio phasing. With the introduction of in-house Cr X-ray sources, these methods benefit from the enhanced anomalous scattering of S and halide atoms, respectively. Here, these methods were combined to determine the crystal structure of BsDegV, a DegV protein-family member from Bacillus subtilis. The protein was cocrystallized with bromide and low-redundancy data were collected to 2.5 A resolution using Cr Kalpha radiation. 17 heavy-atom sites (ten sulfurs and seven bromides) were located using standard methods. The anomalous scattering of some of the BsDegV S atoms and Br atoms was weak, thus neither sulfurs nor bromides could be used alone for structure determination using the collected data. When all 17 heavy-atom sites were used for SAD phasing, an easily interpretable electron-density map was obtained after density modification. The model of BsDegV was built automatically and a palmitate was found tightly bound in the active site. Sequence alignment and comparisons with other known DegV structures provided further insight into the specificity of fatty-acid selection and recognition within this protein family.

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Section: Discussionmentioning

confidence: 63%

Section: Introductionmentioning

confidence: 99%

Structure of a fatty acid-binding protein fromBacillus subtilisdetermined by sulfur-SAD phasing using in-house chromium radiation

Nan

Zhou

Yang

et al. 2009

Acta Crystallogr D Biol Cryst

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“…The adaptive character of both of the cusS and rpoB are indicated by the fact that they are non-synonymous mutations that occur within active sites of their enzymes. The cusS mutation is found in the histidine-kinase, DNA gyrase B, and HSP90-like ATPase domain of the protein (Li et al, 2008 ; ecogene 1 ). The rpoB mutation occurs within the Rpb2 domain 3 site of the RNA polymerase B (Cramer et al, 2001 ; ecogene 2 ).…”

Section: Discussionmentioning

confidence: 99%

Rapid evolution of silver nanoparticle resistance in Escherichia coli

et al. 2015

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The recent exponential increase in the use of engineered nanoparticles (eNPs) means both greater intentional and unintentional exposure of eNPs to microbes. Intentional use includes the use of eNPs as biocides. Unintentional exposure results from the fact that eNPs are included in a variety of commercial products (paints, sunscreens, cosmetics). Many of these eNPs are composed of heavy metals or metal oxides such as silver, gold, zinc, titanium dioxide, and zinc oxide. It is thought that since metallic/metallic oxide NPs impact so many aspects of bacterial physiology that it will difficult for bacteria to evolve resistance to them. This study utilized laboratory experimental evolution to evolve silver nanoparticle (AgNP) resistance in the bacterium Escherichia coli (K-12 MG1655), a bacterium that does not harbor any known silver resistance elements. After 225 generations of exposure to the AgNP environment, the treatment populations demonstrated greater fitness vs. control strains as measured by optical density (OD) and colony forming units (CFU) in the presence of varying concentrations of 10 nm citrate-coated silver nanoparticles (AgNP) or silver nitrate (AgNO3). Genomic analysis shows that changes associated with AgNP resistance were already accumulating within the treatment populations by generation 100, and by generation 200 three mutations had swept to high frequency in the AgNP resistance stocks. This study indicates that despite previous claims to the contrary bacteria can easily evolve resistance to AgNPs, and this occurs by relatively simple genomic changes. These results indicate that care should be taken with regards to the use of eNPs as biocides as well as with regards to unintentional exposure of microbial communities to eNPs in waste products.

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“…Data were collected according to the SECSG S-SAD datacollection protocol (Rose et al, 2004;Li et al, 2008). A 360 data set (D1) was collected using 1 oscillation steps, a crystalto-detector distance of 125 mm and a 3 s exposure time (using a highly attenuated X-ray beam).…”

Section: Data Collection and Processingmentioning

confidence: 99%

Structure of theArchaeoglobus fulgidusorphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal

Zhu

Chen

et al. 2012

Acta Crystallogr D Biol Cryst

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The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ÁF anom /F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360 data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R free = 26.8%) to 2.3 Å resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R free = 21.4%) to 1.85 Å resolution (PDB entry 3ov8). AF1382 has a winged-helix-turn-helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1-82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.

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Crystal structure of a novel non‐Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S‐SAD using a Cr X‐ray source

Cited by 8 publications

References 30 publications

Structure of a fatty acid-binding protein fromBacillus subtilisdetermined by sulfur-SAD phasing using in-house chromium radiation

Structure of a fatty acid-binding protein fromBacillus subtilisdetermined by sulfur-SAD phasing using in-house chromium radiation

Rapid evolution of silver nanoparticle resistance in Escherichia coli

Structure of theArchaeoglobus fulgidusorphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal

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