The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction
Open accessAbstract
Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 Å resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an “arm” structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,715
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,578
PHENIX : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361
Svergun, D., Barberato, C., & Koch, M. H. J. (1995) · Journal of Applied Crystallography · doi:10.1107/s0021889895007047 · Cited by 3,434
de La Fortelle, E., & Bricogne, G. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76073-7 · Cited by 1,892
REFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use
Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F., & Murshudov, G. N. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904023510 · Cited by 1,350
PHYTOCHROME STRUCTURE AND SIGNALING MECHANISMS
Rockwell, N. C., Su, Y.-S., & Lagarias, J. C. (2006) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.56.032604.144208 · Cited by 1,088
[29] Preparation of selenomethionyl proteins for phase determination
Doublié, S. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76075-0 · Cited by 850
Cited by
Structure and function of plant photoreceptors
Möglich, A., Yang, X., Ayers, R. A., & Moffat, K. (2010) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042809-112259 · Cited by 499
Self-citation
Metadata
- Authors
- Yang, X., Kuk, J., & Moffat, K.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2008-09-23
- Volume
- 105
- Issue
- 38
- Pages
- 14715-14720
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2163280837
- Cited by
- 316
- References
- 39
- FWCI
- 26.22
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction. https://app.cochat.ai/papers/10.1073/pnas.0806718105
- The paper
- Yang, X., Kuk, J., & Moffat, K. (2008). Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0806718105
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.