8AG8 | pdb_00008ag8

Structure of the Fluorescence Recovery-like protein FRPL from Pseudomonas borbori

• PDB DOI: https://doi.org/10.2210/pdb8AG8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Pseudomonas borbori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-19 Released: 2023-04-05 
• Deposition Author(s): Weiland, P., Bange, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection.

Steube, N., Moldenhauer, M., Weiland, P., Saman, D., Kilb, A., Ramirez Rojas, A.A., Garg, S.G., Schindler, D., Graumann, P.L., Benesch, J.L.P., Bange, G., Friedrich, T., Hochberg, G.K.A.

(2023) Nat Ecol Evol 7: 756-767

• PubMed: 37012377 
• DOI: https://doi.org/10.1038/s41559-023-02018-8
• Primary Citation Related Structures: 
  8AG8


• PubMed Abstract: 
  

  Highly specific interactions between proteins are a fundamental prerequisite for life, but how they evolve remains an unsolved problem. In particular, interactions between initially unrelated proteins require that they evolve matching surfaces. It is unclear whether such surface compatibilities can only be built by selection in small incremental steps, or whether they can also emerge fortuitously. Here, we used molecular phylogenetics, ancestral sequence reconstruction and biophysical characterization of resurrected proteins to retrace the evolution of an allosteric interaction between two proteins that act in the cyanobacterial photoprotection system. We show that this interaction between the orange carotenoid protein (OCP) and its unrelated regulator, the fluorescence recovery protein (FRP), evolved when a precursor of FRP was horizontally acquired by cyanobacteria. FRP's precursors could already interact with and regulate OCP even before these proteins first encountered each other in an ancestral cyanobacterium. The OCP-FRP interaction exploits an ancient dimer interface in OCP, which also predates the recruitment of FRP into the photoprotection system. Together, our work shows how evolution can fashion complex regulatory systems easily out of pre-existing components.

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Organizational Affiliation: 
• Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany.
Department of Chemistry, University of Marburg, Marburg, Germany.
Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
Department of Chemistry, Oxford University, Oxford, UK.
Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK.
Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany. [e-mail].
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].
Department of Chemistry, University of Marburg, Marburg, Germany. [e-mail].
Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.61 kDa 
• Atom Count: 952 
• Modeled Residue Count: 106 
• Deposited Residue Count: 113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescence Recovery-like protein	A	113	Pseudomonas borbori	Mutation(s): 0  Gene Names: SAMN05216190_11792
UniProt
Find proteins for A0A1I5SVP7 (Pseudomonas borbori) Explore A0A1I5SVP7  Go to UniProtKB:  A0A1I5SVP7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.232 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.46	α = 90
b = 53.46	β = 90
c = 92.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Weiland, P., Bange, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2023-04-12
  Changes: Database references
• Version 1.2: 2023-05-24
  Changes: Database references
• Version 1.3: 2024-02-07
  Changes: Data collection, Refinement description