Stigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289H mutant, room temperature structure

  • Classification: SIGNALING PROTEIN
  • Organism(s): Stigmatella aurantiaca DW4/3-1
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-10-16 Released: 2018-09-19 
  • Deposition Author(s): Schmidt, M., Stojkovic, E.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Eye Institute (NIH/NEI), Academy of Finland

Experimental Data Snapshot

  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome.

Woitowich, N.C.Halavaty, A.S.Waltz, P.Kupitz, C.Valera, J.Tracy, G.Gallagher, K.D.Claesson, E.Nakane, T.Pandey, S.Nelson, G.Tanaka, R.Nango, E.Mizohata, E.Owada, S.Tono, K.Joti, Y.Nugent, A.C.Patel, H.Mapara, A.Hopkins, J.Duong, P.Bizhga, D.Kovaleva, S.E.St Peter, R.Hernandez, C.N.Ozarowski, W.B.Roy-Chowdhuri, S.Yang, J.H.Edlund, P.Takala, H.Ihalainen, J.Brayshaw, J.Norwood, T.Poudyal, I.Fromme, P.Spence, J.C.H.Moffat, K.Westenhoff, S.Schmidt, M.Stojkovic, E.A.

(2018) IUCrJ 5: 619-634

  • DOI: https://doi.org/10.1107/S2052252518010631
  • Primary Citation of Related Structures:  
    6BAF, 6BAK, 6BAO, 6BAP, 6BAY

  • PubMed Abstract: 

    Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxo-bacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.

  • Organizational Affiliation

    Department of Biology, Northeastern Illinois University, Chicago, IL, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photoreceptor-histidine kinase BphP
A, B, C
515Stigmatella aurantiaca DW4/3-1Mutation(s): 1 
Gene Names: STAUR_8015STIAU_3396
Find proteins for Q097N3 (Stigmatella aurantiaca (strain DW4/3-1))
Explore Q097N3 
Go to UniProtKB:  Q097N3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ097N3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BLR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
C33 H36 N4 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.23α = 90
b = 84.23β = 90
c = 477.99γ = 120
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesSTC-1231306
National Science Foundation (NSF, United States)United StatesBIO-MCB 1413360
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT34 GM105549-01 NU-STARS
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY024363
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM095583
Academy of FinlandFinland296135
Academy of FinlandFinland285461

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description