7Z9E

Deinococcus radiodurans BphP PAS-GAF H260A/Y263F mutant

PDB DOI: https://doi.org/10.2210/pdb7Z9E/pdb

Classification: TRANSFERASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-03-21 Released: 2022-08-10
Deposition Author(s): Takala, H.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.169
R-Value Work: 0.128
R-Value Observed: 0.130

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome.

Lehtivuori, H., Rumfeldt, J., Mustalahti, S., Kurkinen, S., Takala, H.

(2022) Photochem Photobiol Sci 21: 1975-1989

PubMed: 35906527 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s43630-022-00272-6
Primary Citation of Related Structures:
7Z9D, 7Z9E

PubMed Abstract:
Phytochromes are red light-sensing photoreceptor proteins that bind a bilin chromophore. Here, we investigate the role of a conserved histidine (H260) and tyrosine (Y263) in the chromophore-binding domain (CBD) of Deinococcus radiodurans phytochrome (DrBphP). Using crystallography, we show that in the H260A variant, the missing imidazole side chain leads to increased water content in the binding pocket. On the other hand, Y263F mutation reduces the water occupancy around the chromophore. Together, these changes in water coordination alter the protonation and spectroscopic properties of the biliverdin. These results pinpoint the importance of this conserved histidine and tyrosine, and the related water network, for the function and applications of phytochromes.

Organizational Affiliation

Nanoscience Center, Department of Physics, University of Jyvaskyla, 40014, Jyvaskyla, Finland.

Macromolecule Content

Total Structure Weight: 38.15 kDa
Atom Count: 2,916
Modelled Residue Count: 309
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome	A	343	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 2 Gene Names: bphP, DR_A0050 EC: 2.7.13.3
UniProt
Find proteins for Q9RZA4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RZA4 Go to UniProtKB: Q9RZA4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RZA4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBV (Subject of Investigation/LOI) Query on LBV Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid C₃₃ H₃₇ N₄ O₆ DKMLMZVDTGOEGU-ISEYCTJISA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A]	C [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A]