5AJ9

G7 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 3.0 of the entry. See complete history

Literature

Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset.

Miton, C.M.Jonas, S.Fischer, G.Duarte, F.Mohamed, M.F.van Loo, B.Kintses, B.Kamerlin, S.C.L.Tokuriki, N.Hyvonen, M.Hollfelder, F.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E7293-E7302

  • DOI: 10.1073/pnas.1607817115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the ac ...

    The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Structural, kinetic, and in silico characterizations of the evolutionary intermediates revealed that two key mutations, T50A and M72V, locally reshaped the active site, improving access to the catalytic machinery for the phosphonate. Measured transition state (TS) charge changes along the trajectory suggest the creation of a new Michaelis complex (E•S, enzyme-substrate), with enhanced leaving group stabilization in the TS for the promiscuous phosphonate ( β leaving group from -1.08 to -0.42). Rather than altering the catalytic machinery, evolutionary repurposing was achieved by fine-tuning the molecular recognition of the phosphonate in the Michaelis complex, and by extension, also in the TS. This molecular scenario constitutes a mechanistic alternative to adaptation solely based on enzyme flexibility and conformational selection. Instead, rapid functional transitions between distinct chemical reactions rely on the high reactivity of permissive active-site architectures that allow multiple substrate binding modes.


    Organizational Affiliation

    Department of Chemistry, Biomedicinskt Centrum (BMC), Uppsala University, 751 23 Uppsala, Sweden.,Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom; fh111@cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ARYLSULFATASE
A, B
536Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 8 
Gene Names: atsA
EC: 3.1.6.1
Find proteins for P51691 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P51691
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDZ
Query on DDZ
A, B
L-PEPTIDE LINKINGC3 H7 N O4ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.399α = 90.00
b = 66.496β = 93.84
c = 89.435γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
AutoPROCdata reduction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Advisory, Data collection, Database references
  • Version 2.0: 2019-01-30
    Type: Advisory, Atomic model, Data collection, Derived calculations
  • Version 3.0: 2019-04-24
    Type: Data collection, Derived calculations, Polymer sequence