3KIF

The crystal structures of two fragments truncated from 5-bladed beta-propeller lectin, tachylectin-2 (Lib1-B7-18 and Lib2-D2-15)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metamorphic proteins mediate evolutionary transitions of structure

Yadid, I.Kirshenbaum, N.Sharon, M.Dym, O.Tawfik, D.S.

(2010) Proc.Natl.Acad.Sci.USA 107: 7287-7292

  • DOI: 10.1073/pnas.0912616107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The primary sequence of proteins usually dictates a single tertiary and quaternary structure. However, certain proteins undergo reversible backbone rearrangements. Such metamorphic proteins provide a means of facilitating the evolution of new folds a ...

    The primary sequence of proteins usually dictates a single tertiary and quaternary structure. However, certain proteins undergo reversible backbone rearrangements. Such metamorphic proteins provide a means of facilitating the evolution of new folds and architectures. However, because natural folds emerged at the early stages of evolution, the potential role of metamorphic intermediates in mediating evolutionary transitions of structure remains largely unexplored. We evolved a set of new proteins based on approximately 100 amino acid fragments derived from tachylectin-2--a monomeric, 236 amino acids, five-bladed beta-propeller. Their structures reveal a unique pentameric assembly and novel beta-propeller structures. Although identical in sequence, the oligomeric subunits adopt two, or even three, different structures that together enable the pentameric assembly of two propellers connected via a small linker. Most of the subunits adopt a wild-type-like structure within individual five-bladed propellers. However, the bridging subunits exhibit domain swaps and asymmetric strand exchanges that allow them to complete the two propellers and connect them. Thus, the modular and metamorphic nature of these subunits enabled dramatic changes in tertiary and quaternary structure, while maintaining the lectin function. These oligomers therefore comprise putative intermediates via which beta-propellers can evolve from smaller elements. Our data also suggest that the ability of one sequence to equilibrate between different structures can be evolutionary optimized, thus facilitating the emergence of new structures.


    Organizational Affiliation

    Department of Biological Chemistry, and Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-bladed beta-propeller lectin
A, B, C, D, E, F, G, H, I, J
106Tachypleus tridentatusMutation(s): 0 
Find proteins for Q27084 (Tachypleus tridentatus)
Go to UniProtKB:  Q27084
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
E, J
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GDL
Query on GDL

Download SDF File 
Download CCD File 
A, B, D, E, F, G, I, J
2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
C8 H13 N O6
NELQYZRSPDCGRQ-DBRKOABJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 80.558α = 90.00
b = 80.558β = 90.00
c = 170.681γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-26
    Type: Database references
  • Version 1.3: 2014-03-19
    Type: Source and taxonomy, Structure summary