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Structure of a fatty-acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiation

Nan, Jie LU ; Zhou, Yanfeng ; Yang, Cheng ; Brostromer, Erik ; Kristensen, Ole and Su, Xiao Dong LU (2009) In Acta Crystallographica. Section D: Biological Crystallography 65(Pt 5). p.8-440
Abstract

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... (More)

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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author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
keywords
Amino Acid Sequence, Bacillus subtilis, Bacterial Proteins, Binding Sites, Bromides, Chromium, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Palmitates, Protein Conformation, Recombinant Fusion Proteins, Sequence Alignment, Sequence Homology, Amino Acid, Sulfur
in
Acta Crystallographica. Section D: Biological Crystallography
volume
65
issue
Pt 5
pages
9 pages
publisher
John Wiley & Sons Inc.
external identifiers
  • pmid:19390149
  • scopus:65349090174
ISSN
1399-0047
DOI
10.1107/S0907444909007756
language
English
LU publication?
yes
id
c04bff95-9f00-492a-bc3a-4d95dcc50036
date added to LUP
2016-09-07 22:53:04
date last changed
2023-11-07 16:26:42
@article{c04bff95-9f00-492a-bc3a-4d95dcc50036,
  abstract     = {{<p>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.</p>}},
  author       = {{Nan, Jie and Zhou, Yanfeng and Yang, Cheng and Brostromer, Erik and Kristensen, Ole and Su, Xiao Dong}},
  issn         = {{1399-0047}},
  keywords     = {{Amino Acid Sequence; Bacillus subtilis; Bacterial Proteins; Binding Sites; Bromides; Chromium; Crystallography, X-Ray; Models, Molecular; Molecular Sequence Data; Palmitates; Protein Conformation; Recombinant Fusion Proteins; Sequence Alignment; Sequence Homology, Amino Acid; Sulfur}},
  language     = {{eng}},
  number       = {{Pt 5}},
  pages        = {{8--440}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Acta Crystallographica. Section D: Biological Crystallography}},
  title        = {{Structure of a fatty-acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiation}},
  url          = {{http://dx.doi.org/10.1107/S0907444909007756}},
  doi          = {{10.1107/S0907444909007756}},
  volume       = {{65}},
  year         = {{2009}},
}