3TP4

Crystal Structure of engineered protein at the resolution 1.98A, Northeast Structural Genomics Consortium Target OR128


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.979 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 

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:  3V45, 4DRT, 4ESS, 4ETJ, 4ETK, 4F2V, 4JCA, 4JLL, 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].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
computational Design of Enzyme
A, B
475N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.979 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.666α = 90.00
b = 113.943β = 90.00
c = 116.815γ = 90.00
Software Package:
Software NamePurpose
BALBESphasing
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references
  • Version 1.2: 2014-05-14
    Type: Database references