YbtT - Type II thioesterase from Yersiniabactin NRPS/PKS biosynthetic pathway

Experimental Data Snapshot

  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


YbtT is a low-specificity type II thioesterase that maintains production of the metallophore yersiniabactin in pathogenic enterobacteria.

Ohlemacher, S.I.Xu, Y.Kober, D.L.Malik, M.Nix, J.C.Brett, T.J.Henderson, J.P.

(2018) J. Biol. Chem. 293: 19572-19585

  • DOI: 10.1074/jbc.RA118.005752
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clinical isolates of <i>Yersinia </i>, <i>Klebsiella </i>, and <i>Escherichia coli </i> frequently secrete the small molecule metallophore yersiniabactin (Ybt), which passivates and scavenges transition metals during human infections. YbtT is enco ...

    Clinical isolates of Yersinia , Klebsiella , and Escherichia coli frequently secrete the small molecule metallophore yersiniabactin (Ybt), which passivates and scavenges transition metals during human infections. YbtT is encoded within the Ybt biosynthetic operon and is critical for full Ybt production in bacteria. However, its biosynthetic function has been unclear because it is not essential for Ybt production by the in vitro reconstituted nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) pathway. Here, we report the structural and biochemical characterization of YbtT. YbtT structures at 1.4-1.9 Å resolution possess a serine hydrolase catalytic triad and an associated substrate chamber with features similar to those previously reported for low-specificity type II thioesterases (TEIIs). We found that YbtT interacts with the two major Ybt biosynthetic proteins, HMWP1 (high-molecular-weight protein 1) and HMWP2 (high-molecular-weight protein 2), and hydrolyzes a variety of aromatic and acyl groups from their phosphopantetheinylated carrier protein domains. In vivo YbtT titration in uropathogenic E. coli revealed a distinct optimum for Ybt production consistent with a tradeoff between clearing both stalled inhibitory intermediates and productive Ybt precursors from HMWP1 and HMWP2. These results are consistent with a model in which YbtT maintains cellular Ybt biosynthesis by removing nonproductive, inhibitory thioesters that form aberrantly at multiple sites on HMWP1 and HMWP2.

    Organizational Affiliation

    Division of Infectious Diseases.,From the Center for Women's Infectious Diseases Research, hendersonj@wustl.edu.,Department of Internal Medicine, and.,Department of Internal Medicine, and tbrett@wustl.edu.,From the Center for Women's Infectious Diseases Research.,the Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63110 and.,Division of Pulmonary and Critical Care Medicine.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron aquisition yersiniabactin synthesis enzyme, YbtT
292Escherichia coliMutation(s): 0 
Gene Names: irp4 (srfAD, ybtT)
EC: 3.1.2.-
Find proteins for A0A061LQM0 (Escherichia coli)
Go to UniProtKB:  A0A061LQM0
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 82.301α = 90.00
b = 82.301β = 90.00
c = 81.935γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK099534
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL119813

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references
  • Version 1.2: 2019-01-02
    Type: Data collection, Database references
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence