6KJR

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: 2.36 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.2 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 142: 16031-16038

  • DOI: https://doi.org/10.1021/jacs.0c07331
  • Primary Citation of Related Structures:  
    6KJH, 6KJJ, 6KJP, 6KJQ, 6KJR, 6KJT

  • 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 in overcoming multi-drug-resistant bacteria. However, which enzyme catalyzes this reaction remains enigmatic. Herein, we deciphered a β-lactamase homologue 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 toward acyl acceptors with different scaffolds. The crystal structure of BmmI covalently linked to the succinyl group and systematic mutagenesis highlighted the role of oxyanion holelike geometry in the recognition of carboxyl-terminated acyl donors. The engineering of this geometry expanded its substrate scope, with the R166A/G/Q variants recognizing up to C12 alkyl acid thioester. The structure of BmmI with acyl acceptor MLN A revealed the importance of Arg292 in the recognition of macrolide substrates. Moreover, the mechanism of the 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 the substrate selectivity of acyltransferases, which would guide rational enzyme engineering for drug development.


  • Organizational Affiliation

    Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative beta-lactamase391Jeotgalibacillus marinusMutation(s): 1 
Gene Names: mlnI
UniProt
Find proteins for A0A0U1X4V6 (Jeotgalibacillus marinus)
Explore A0A0U1X4V6 
Go to UniProtKB:  A0A0U1X4V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1X4V6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D9O (Subject of Investigation/LOI)
Query on D9O

Download Ideal Coordinates CCD File 
B [auth A]4-[[(3~{E},5~{Z},8~{S},9~{E},11~{E},14~{S},16~{R},17~{Z},19~{E},24~{R})-24-methyl-14,16-bis(oxidanyl)-2-oxidanylidene-1-oxacyclotetracosa-3,5,9,11,17,19-hexaen-8-yl]oxy]-4-oxidanylidene-butanoic acid
C28 H38 O8
QPJULYYJHQTWML-RJAZCIHLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.190 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.947α = 90
b = 117.947β = 90
c = 52.222γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description