5OD9 | pdb_00005od9

Structure of the engineered metalloesterase MID1sc9

• PDB DOI: https://doi.org/10.2210/pdb5OD9/pdb

• Classification: DE NOVO PROTEIN HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-05 Released: 2018-12-12 
• Deposition Author(s): Studer, S., Mittl, P.R.E., Hilvert, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.191 (DCC) 
• R-Value Work: 
  0.151 (DCC) 

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

• PubMed: 30545884 
• DOI: https://doi.org/10.1126/science.aau3744
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7365, USA.
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.64 kDa 
• Atom Count: 1,860 
• Modeled Residue Count: 183 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MID1sc9	A, B	97	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9RW	L [auth A]	(2~{S})-2-phenylpropanoic acid C9 H10 O2 YPGCWEMNNLXISK-ZETCQYMHSA-N
IMD	K [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], D [auth A], M [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.191 (DCC) 
• R-Value Work:  0.151 (DCC) 

Diffraction Data: https://doi.org/10.18430/m35od9

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.82	α = 90
b = 104.959	β = 90
c = 33.604	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Studer, S., Mittl, P.R.E., Hilvert, D.

Revision History  

• 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
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations