7E2T

Synechocystis GUN4 in complex with phycocyanobilin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of bilin binding by the chlorophyll biosynthesis regulator GUN4.

Hu, J.H.Chang, J.W.Xu, T.Wang, J.Wang, X.Lin, R.Duanmu, D.Liu, L.

(2021) Protein Sci 30: 2083-2091

  • DOI: https://doi.org/10.1002/pro.4164
  • Primary Citation of Related Structures:  
    7E2R, 7E2S, 7E2T, 7E2U

  • PubMed Abstract: 

    The chlorophyll biosynthesis regulator GENOMES UNCOUPLED 4 (GUN4) is conserved in nearly all oxygenic photosynthetic organisms. Recently, GUN4 has been found to be able to bind the linear tetrapyrroles (bilins) and stimulate the magnesium chelatase activity in the unicellular green alga Chlamydomonas reinhardtii. Here, we characterize GUN4 proteins from Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 for their ability to bind bilins, and present the crystal structures of Synechocystis GUN4 in biliverdin-bound, phycocyanobilin-bound, and phytochromobilin-bound forms at the resolutions of 1.05, 1.10, and 1.70 Å, respectively. These linear molecules adopt a cyclic-helical conformation, and bind more tightly than planar porphyrins to the tetrapyrrole-binding pocket of GUN4. Based on structural comparison, we propose a working model of GUN4 in regulation of tetrapyrrole biosynthetic pathway, and address the role of the bilin-bound GUN4 in retrograde signaling.


  • Organizational Affiliation

    School of Life Sciences, Anhui University, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ycf53-like protein233Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: sll0558
UniProt
Find proteins for P72583 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P72583 
Go to UniProtKB:  P72583
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72583
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UYC (Subject of Investigation/LOI)
Query on UYC

Download Ideal Coordinates CCD File 
B [auth A]3-[2-[(~{Z})-[5-[(~{Z})-[(4~{R})-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid
C33 H38 N4 O6
XAVVMXGLKJSJDU-NSNBCYBJSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.465α = 90
b = 64.695β = 90
c = 106.521γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2021-08-25 
  • Deposition Author(s): Liu, L., Hu, J.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0503703

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description