6BA8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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:  
    6BA8, 6BA9

  • PubMed Abstract: 
  • 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 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

    Department of Internal Medicine, and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iron aquisition yersiniabactin synthesis enzyme, YbtTA292Escherichia coliMutation(s): 0 
Gene Names: 
irp4srfADA4T40_14730AML07_28155AUS26_21405AW106_20985ECONIH1_11380ERS085406_04094ERS150876_03959FORC28_2175MS6198_22290SK85_02209WM48_10340ybtTA6V01_16390AWF59_018825AZZ83_004484B6V57_10495BvCmsKKP061_00546BvCmsKSP045_04430BvCmsKSP067_02899BvCmsSINP011_04182C2U48_24685C4K41_21265C4M78_09685C6B13_18455C7B02_06990C9306_18535C9Z89_17290CO706_07405CRM83_03040CT146_21395D3C88_12360D3P02_15640D5H35_15745D6004_17105D9610_14695D9H10_14820D9I20_10555DAH32_20405DB359_03860DIV22_11715DL530_15315DL979_00140DLW60_16515DM102_02585DM155_15990DNR41_00145DQF57_19875DQF71_17650DS143_17095DS966_21715DU309_17840DU333_03030DW236_02520E2114_13480E2115_13940E2148_19635EA189_00140EA198_02380EA200_00140EA214_01945EA218_16810EA231_03685EA235_09845EA242_21840EA245_13060EA250_03470EAM59_20420EAN70_19975EBM08_20240ED600_16130EG599_19920EI032_11835EIA08_14930EKI52_25845ELT23_21450ELT33_08255ELY48_05350EPS94_00275EPU41_11350EQ823_15140EQO00_10475EWK56_23660F7F00_18535F7F23_18300F7F26_19830F9059_13225F9X20_19985FAF34_028090FPI65_12170FQU83_12075FZN06_15895GFU40_00265GFU45_09775GFU47_04605GKE15_01895GKE16_01895GKE22_01895GKE24_01895GKE26_01895GKE29_19115GKE31_01895GKE39_01895GKE46_01895GKE53_01895GKE58_00135GKE60_01895GKE64_01895GKE69_17480GKE77_01900GKE79_01895GKE87_21705GKE92_14745GKE93_04890GKE98_02435GKF89_19095GP666_12190GP935_03525GQE33_07830GQE36_08195GQE58_02905GQY14_20195HmCmsJML074_02943HmCmsJML146_04173NCTC10865_02596NCTC8960_04784NCTC9075_02775NCTC9434_01981RX35_00871SAMEA3753300_03054

EC: 3.1.2
Find proteins for A0A061LQM0 (Escherichia coli)
Explore A0A061LQM0 
Go to UniProtKB:  A0A061LQM0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 4 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/631 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.301α = 90
b = 82.301β = 90
c = 81.935γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-02
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence