4U9E

Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A designed supramolecular protein assembly with in vivo enzymatic activity

Song, W.J.Tezcan, A.F.

(2014) Science 346: 1525

  • DOI: 10.1126/science.1259680
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an art ...

    The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an artificial metallo-β-lactamase, constructed via the self-assembly of a structurally and functionally unrelated, monomeric redox protein into a tetrameric assembly that possesses catalytic zinc sites in its interfaces. The designed metallo-β-lactamase is functional in the Escherichia coli periplasm and enables the bacteria to survive treatment with ampicillin. In vivo screening of libraries has yielded a variant that displays a catalytic proficiency [(k(cat)/K(m))/k(uncat)] for ampicillin hydrolysis of 2.3 × 10(6) and features the emergence of a highly mobile loop near the active site, a key component of natural β-lactamases to enable substrate interactions.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562
A
106Escherichia coliMutation(s): 16 
Gene Names: cybC
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.313α = 90.00
b = 92.213β = 90.00
c = 98.599γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE1306646

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations, Source and taxonomy