5OD1

Structure of the engineered metalloesterase MID1sc10 complexed with a phosphonate transition state analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.129 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Evolution of a highly active and enantiospecific metalloenzyme from short peptides.

Studer, S.Hansen, D.A.Pianowski, Z.L.Mittl, P.R.E.Debon, A.Guffy, S.L.Der, B.S.Kuhlman, B.Hilvert, D.

(2018) Science 362: 1285-1288

  • DOI: https://doi.org/10.1126/science.aau3744

  • PubMed Abstract: 

    Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency ( k cat / K M ~ 10 6 M -1 s -1 ). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.


  • Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MID1sc1097synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9RQ
Query on 9RQ

Download Ideal Coordinates CCD File 
C [auth A][2-oxidanylidene-7-[oxidanyl-[(1~{S})-1-phenylethyl]phosphoryl]oxy-chromen-4-yl]methanesulfonic acid
C18 H17 O8 P S
HLYLTMSHSJKDCP-LBPRGKRZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.349α = 90
b = 46.877β = 90
c = 112.621γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.3: 2020-04-22
    Changes: Database references