4JLL

Crystal Structure of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1 covalently bound with FP-alkyne, Northeast Structural Genomics Consortium (NESG) Target OR273


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design of activated serine-containing catalytic triads with atomic-level accuracy.

Rajagopalan, S.Wang, C.Yu, K.Kuzin, A.P.Richter, F.Lew, S.Miklos, A.E.Matthews, M.L.Seetharaman, J.Su, M.Hunt, J.F.Cravatt, B.F.Baker, D.

(2014) Nat Chem Biol 10: 386-391

  • DOI: 10.1038/nchembio.1498
  • Primary Citation of Related Structures:  
    4DRT, 4F2V, 4ESS, 4ETK, 4ETJ, 4JCA, 4JLL, 3TP4, 3V45, 4JVV

  • PubMed Abstract: 
  • A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successfu ...

    A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.


    Organizational Affiliation

    1] Department of Biochemistry, University of Washington, Seattle, Washington, United States. [2] Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, USA. [3] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Evolved variant of computationally designed serine hydrolase OSH55.4_H1A167synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SEF
Query on SEF

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A
ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate
C20 H37 F N O4 P
JFCFPSBLBVUKMV-HHHXNRCGSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.846α = 90
b = 66.977β = 100.27
c = 37.911γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-05-14
    Changes: Database references