6WZ1

Mn-bound structure of an engineered protein trimer, TriCyt3

  • Classification: METAL BINDING PROTEIN
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2020-05-13 Released: 2020-09-16 
  • Deposition Author(s): Tezcan, F.A., Kakkis, A.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report



Literature

Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites.

Tezcan, F.A.Kakkis, A.Gagnon, D.Esselborn, J.Britt, R.D.

(2020) Angew Chem Int Ed Engl 

  • DOI: 10.1002/anie.202009226
  • Primary Citation of Related Structures:  
    6X7E, 6X8X, 6WZ2, 6WZ1, 6WZ3, 6WYU, 6WZ7, 6WZ0, 6WZA, 6WZC

  • PubMed Abstract: 
  • To mimic a hypothetical pathway ...

    To mimic a hypothetical pathway for protein evolution, we previously developed a design strategy (Metal-Templated Interface Redesign), in which a monomeric protein (cytochrome cb562) was tailored for metal-mediated self-assembly, followed by the re-design of the resulting oligomers for enhanced stability and metal-based functions. Here we show that a single hydrophobic mutation on the cytochrome cb562 surface can drastically alter the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1)3, featuring an unusual hexa-histidine coordination motif. Through computational and rational redesign, this nascent trimer is converted into second and third-generation variants (TriCyt2)3 and (TriCyt3)3 with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique design platform to a) provide tunable coupling between protein quaternary structure and metal coordination, b) enable the construction of metal/pH-switchable protein oligomerization motifs, and c) generate a robust metal coordination site that can accommodate all mid-to-late first-row transition metal ions with high affinity, including Mn(II) with nanomolar dissociation constants,  rivaling those of the strongest Mn(II)-binding protein, calprotectin. 

    .


    Organizational Affiliation

    University of California Davis, Chemistry, UNITED STATES.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562A, B, C106Escherichia coliMutation(s): 16 
Gene Names: cybC
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download CCD File 
A, B, C
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.759α = 90
b = 77.392β = 110.7
c = 47.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE1607145
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM112584-01

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release