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 5NO5 | pdb_00005no5

AbyA5 Wildtype


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.261 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NO5

This is version 1.3 of the entry. See complete history. 

Literature

An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis.

Lees, N.R., Han, L.C., Byrne, M.J., Davies, J.A., Parnell, A.E., Moreland, P.E.J., Stach, J.E.M., van der Kamp, M.W., Willis, C.L., Race, P.R.

(2019) Angew Chem Int Ed Engl 58: 2305-2309

  • DOI: https://doi.org/10.1002/anie.201812105
  • Primary Citation Related Structures: 
    4YWF, 5NO5

  • PubMed Abstract: 

    Spirotetronate and spirotetramate natural products include a multitude of compounds with potent antimicrobial and antitumor activities. Their biosynthesis incorporates many unusual biocatalytic steps, including regio- and stereo-specific modifications, cyclizations promoted by Diels-Alderases, and acetylation-elimination reactions. Here we focus on the acetate elimination catalyzed by AbyA5, implicated in the formation of the key Diels-Alder substrate to give the spirocyclic system of the antibiotic abyssomicin C. Using synthetic substrate analogues, it is shown that AbyA5 catalyzes stereospecific acetate elimination, establishing the (R)-tetronate acetate as a biosynthetic intermediate. The X-ray crystal structure of AbyA5, the first of an acetate-eliminating enzyme, reveals a deviant acetyl esterase fold. Molecular dynamics simulations and enzyme assays show the use of a His-Ser dyad to catalyze either elimination or hydrolysis, via disparate mechanisms, under substrate control.


  • Organizational Affiliation: 
    • School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.

Macromolecule Content 

  • Total Structure Weight: 81.55 kDa 
  • Atom Count: 5,399 
  • Modeled Residue Count: 698 
  • Deposited Residue Count: 748 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AbyA5
A, B
374MicromonosporaMutation(s): 0 
Gene Names: abyA5, VAB18032_16440
UniProt
Find proteins for F4F7F5 (Micromonospora maris (strain DSM 45365 / JCM 31040 / NBRC 109089 / NRRL B-24793 / AB-18-032))
Explore F4F7F5 
Go to UniProtKB:  F4F7F5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4F7F5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.229α = 90
b = 88.36β = 90
c = 131.289γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/D526037/

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description