Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Signaling by a bacterial phytochrome histidine kinase involves a conformational cascade reorganizing the dimeric photoreceptor.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 6853, Year 2024
Publish date	Aug 10, 2024
Authors	E Sethe Burgie / Katherine Basore / Michael J Rau / Brock Summers / Alayna J Mickles / Vadim Grigura / James A J Fitzpatrick / Richard D Vierstra /
PubMed Abstract	Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of ...Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of downstream events are emerging, it remains unclear how Phys translate light into an interpretable conformational signal. Here, we present models of both states for a dimeric Phy with histidine kinase (HK) activity from the proteobacterium Pseudomonas syringae, which were built from high-resolution cryo-EM maps (2.8-3.4-Å) of the photosensory module (PSM) and its following signaling (S) helix together with lower resolution maps for the downstream output region augmented by RoseTTAFold and AlphaFold structural predictions. The head-to-head models reveal the PSM and its photointerconversion mechanism with strong clarity, while the HK region is interpretable but relatively mobile. Pr/Pfr comparisons show that bilin phototransformation alters PSM architecture culminating in a scissoring motion of the paired S-helices linking the PSMs to the HK bidomains that ends in reorientation of the paired catalytic ATPase modules relative to the phosphoacceptor histidines. This action apparently primes autophosphorylation enroute to phosphotransfer to the cognate DNA-binding response regulator AlgB which drives quorum-sensing behavior through transient association with the photoreceptor. Collectively, these models illustrate how light absorption conformationally translates into accelerated signaling by Phy-type kinases.
External links	Nat Commun / PubMed:39127720 / PubMed Central
Methods	EM (single particle)
Resolution	2.81 - 3.3 Å
Structure data	41903 8u4x EMDB-41903, PDB-8u4x: Cryo-EM structure of PsBphP in Pr state Method: EM (single particle) / Resolution: 2.81 Å 41941 8u62 EMDB-41941, PDB-8u62: Cryo-EM structure of PsBphP in Pfr state, Dimer of Dimers FL Method: EM (single particle) / Resolution: 3.3 Å 41942 8u63 EMDB-41942, PDB-8u63: Cryo-EM structure of PsBphP in Pfr state, Dimer of Dimers PSM only Method: EM (single particle) / Resolution: 3.01 Å 41943 8u64 EMDB-41943, PDB-8u64: Cryo-EM structure of PsBphP in Pfr state, medial PSM only Method: EM (single particle) / Resolution: 3.13 Å 41944 8u65 EMDB-41944, PDB-8u65: Cryo-EM structure of PsBphP in Pfr state, splayed PSM only Method: EM (single particle) / Resolution: 3.01 Å 42030 8u8z EMDB-42030, PDB-8u8z: Cryo-EM structure of PsBphP in Pr state, extended DHp Method: EM (single particle) / Resolution: 3.25 Å
Chemicals	ChemComp-LBV: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium
Source	pseudomonas syringae pv. tomato str. dc3000 (bacteria)
Keywords	PLANT PROTEIN / Pseudomonas syringae bacteriophytochrome