8J68 | pdb_00008j68

Crystal structure of the LOV1 R60K mutant of Klebsormidium nitens phototropin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.224 (Depositor) 
  • R-Value Work: 
    0.171 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Unusual photodynamic characteristics of the light-oxygen-voltage domain of phototropin linked to terrestrial adaptation of Klebsormidium nitens.

Sharma, S.Gautam, A.K.Singh, R.Gourinath, S.Kateriya, S.

(2024) FEBS J 291: 5156-5176

  • DOI: https://doi.org/10.1111/febs.17284
  • Primary Citation of Related Structures:  
    8I11, 8IL9, 8IYN, 8J68

  • PubMed Abstract: 

    Phototropin (Phot), a blue light-sensing LOV domain protein, mediates blue light responses and is evolutionarily conserved across the green lineage. Klebsormidium nitens, a green terrestrial alga, presents a valuable opportunity to study adaptive responses from aquatic to land habitat transitions. We determined the crystal structure of Klebsormidium nitens Phot LOV1 domain (KnLOV1) in the dark and engineered different mutations (R60K, Q122N, and D33N) to modulate the lifetime of the photorecovery cycle. We observed unusual, slow recovery kinetics in the wild-type KnLOV1 domain (τ = 41 ± 3 min) compared to different mutants (R60K: τ = 2.0 ± 0.1 min, Q122N: τ = 1.7 ± 0.1 min, D33N: τ = 9.6 ± 0.1 min). Crystal structures of wild-type KnLOV1 and mutants revealed subtle but critical changes near the protein chromophore that is responsible for modulating protein dark recovery time. Our findings shed light on the unique structural and biochemical characteristics of the newly studied KnLOV1 and its evolutionary importance for phototropin-mediated physiology.


  • Organizational Affiliation
    • Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phototropin153Klebsormidium nitensMutation(s): 1 
Gene Names: KFL_000480260
EC: 2.7.11.1
UniProt
Find proteins for A0A1Y1HNG4 (Klebsormidium nitens)
Explore A0A1Y1HNG4 
Go to UniProtKB:  A0A1Y1HNG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y1HNG4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.224 (Depositor) 
  • R-Value Work:  0.171 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.905α = 90
b = 53.905β = 90
c = 137.408γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-18
    Changes: Database references