6KJQ

Functional and structural insights into the unusual oxyanion hole-like geometry in macrolactin acyltransferase selective for dicarboxylic acyl donors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis of Specificity for Carboxyl-terminated Acyl Donors in A Bacterial Acyltransferase.

Xiao, F.Dong, S.Liu, Y.Feng, Y.Li, H.Yun, C.H.Cui, Q.Li, W.

(2020) J Am Chem Soc 

  • DOI: 10.1021/jacs.0c07331
  • Primary Citation of Related Structures:  
    6KJQ, 6KJT, 6KJH

  • PubMed Abstract: 
  • Macrolactins (MLNs) are a class of important antimacular degeneration and antitumor agents. Malonylated/succinylated MLNs are even more important due to their efficacy to overcome multidrug resistant bacteria. However, which enzyme catalyzes this rea ...

    Macrolactins (MLNs) are a class of important antimacular degeneration and antitumor agents. Malonylated/succinylated MLNs are even more important due to their efficacy to overcome multidrug resistant bacteria. However, which enzyme catalyzes this reaction remains enigmatic. Herein, we deciphered a beta-lactamase homolog BmmI to be responsible for this step. BmmI could specifically attach C3-C5 alkyl acid thioesters onto 7-OH of MLN A, and also exhibits substrate promiscuity towards acyl acceptors with different scaffolds. Crystal structure of BmmI covalently linked with succinyl group and systematic mutagenesis highlighted the role of an oxyanion hole-like geometry in the recognition of carboxyl-terminated acyl donors. Engineering of this geometry expanded its substrate scope, with the R166A/G/Q variants recognizing up to C12 alkyl acid thioester. Structure of BmmI with the acyl acceptor MLN A revealed the importance of Arg292 in recognition of the macrolide substrates. Moreover, the mechanism of BmmI-catalyzed acyltransfer reaction was established, unmasking the deft role of Lys76 in governing acyl donors as well as catalysis. Our studies uncover the delicate mechanism underlying substrate selectivity of acyltransferases, which would guide rational enzyme engineering for drug development.


    Organizational Affiliation

    Molecular Biology, Princeton University, Princeton, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative beta-lactamaseA391Jeotgalibacillus marinusMutation(s): 2 
Gene Names: mlnI
Find proteins for A0A0U1X4V6 (Jeotgalibacillus marinus)
Explore A0A0U1X4V6 
Go to UniProtKB:  A0A0U1X4V6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D9F
Query on D9F

Download CCD File 
A
(3~{Z},5~{E},8~{S},9~{E},11~{E},14~{S},16~{R},17~{Z},19~{E},24~{R})-24-methyl-8,14,16-tris(oxidanyl)-1-oxacyclotetracosa-3,5,9,11,17,19-hexaen-2-one
C24 H34 O5
XXDIJWSZFWZBRM-LZAGWGSOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.24α = 90
b = 116.24β = 90
c = 50.25γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references