4UPH

Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium radiobacter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 3.2 of the entry. See complete history


Literature

Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily.

van Loo, B.Bayer, C.D.Fischer, G.Jonas, S.Valkov, E.Mohamed, M.F.Vorobieva, A.Dutruel, C.Hyvonen, M.Hollfelder, F.

(2019) J Am Chem Soc 141: 370-387

  • DOI: 10.1021/jacs.8b10290
  • Primary Citation of Related Structures:  
    4UPH, 4UPI, 4UPK, 4UPL

  • PubMed Abstract: 
  • Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily ...

    Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 10 11 - to 10 17 -fold for their primary and 10 9 - to 10 12 -fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. This functional characterization and crystallography reveal a novel class of ASs that is so similar in sequence to known PMHs that it had not been recognized as having diverged in function. Based on analysis of snapshots of catalytic promiscuity "in transition", we develop possible models that would allow functional evolution and determine scenarios for trade-off between multiple activities. For the new ASs, we observe largely invariant substrate specificity that would facilitate the transition from ASs to PMHs via trade-off-free molecular exaptation, that is, evolution without initial loss of primary activity and specificity toward the original substrate. This ability to bypass low activity generalists provides a molecular solution to avoid adaptive conflict.


    Organizational Affiliation

    Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SULFATASE (SULFURIC ESTER HYDROLASE) PROTEINA, B, C, D547Agrobacterium radiobacter K84Mutation(s): 0 
Gene Names: Arad_4766
UniProt
Find proteins for B9JE48 (Agrobacterium radiobacter (strain K84 / ATCC BAA-868))
Explore B9JE48 
Go to UniProtKB:  B9JE48
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDZ
Query on DDZ
A, B, C, DL-PEPTIDE LINKINGC3 H7 N O4ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.69α = 90
b = 232.69β = 90
c = 112.05γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
AutoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2017-09-13
    Changes: Advisory, Data collection
  • Version 1.3: 2018-12-19
    Changes: Data collection, Database references
  • Version 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Derived calculations, Experimental preparation
  • Version 3.0: 2019-04-24
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 3.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 3.2: 2019-07-10
    Changes: Data collection