5OD9

Structure of the engineered metalloesterase MID1sc9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
    5OD1, 5OD9

  • 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
MID1sc9
A, B
97synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9RW
Query on 9RW

Download Ideal Coordinates CCD File 
L [auth A](2~{S})-2-phenylpropanoic acid
C9 H10 O2
YPGCWEMNNLXISK-ZETCQYMHSA-N
IMD
Query on IMD

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K [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN

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C [auth A],
D [auth A],
M [auth A],
N [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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E [auth A],
F [auth A],
O [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.82α = 90
b = 104.959β = 90
c = 33.604γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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