Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.79 kDa 
• Atom Count: 2166 
• Residue Count: 249 
• Unique protein chains: 1

6BA8

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

• DOI: 10.2210/pdb6BA8/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-12 Released: 2018-10-31 
• Deposition Author(s): Brett, T.J., Kober, D.L., Ohlemacher, S.I., Henderson, J.P.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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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 

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

• PubMed: 30355735 
• 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 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.

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Organizational Affiliation: 

Department of Internal Medicine, and.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron aquisition yersiniabactin synthesis enzyme, YbtT	A	292	Escherichia coli	Mutation(s): 0  Gene Names:  irp4, srfAD, A4T40_14730, AML07_28155, AUS26_21405, AW106_20985, ECONIH1_11380, ERS085406_04094, ERS150876_03959, FORC28_2175, MS6198_22290, SK85_02209, WM48_10340, ybtT, A6V01_16390, AWF59_018825, AZZ83_004484, B6V57_10495, BvCmsKKP061_00546, BvCmsKSP045_04430, BvCmsKSP067_02899, BvCmsSINP011_04182, C2U48_24685, C4K41_21265, C4M78_09685, C6B13_18455, C7B02_06990, C9306_18535, C9Z89_17290, CO706_07405, CRM83_03040, CT146_21395, D3C88_12360, D3P02_15640, D5H35_15745, D6004_17105, D9610_14695, D9H10_14820, D9I20_10555, DAH32_20405, DB359_03860, DIV22_11715, DL530_15315, DL979_00140, DLW60_16515, DM102_02585, DM155_15990, DNR41_00145, DQF57_19875, DQF71_17650, DS143_17095, DS966_21715, DU309_17840, DU333_03030, DW236_02520, E2114_13480, E2115_13940, E2148_19635, EA189_00140, EA198_02380, EA200_00140, EA214_01945, EA218_16810, EA231_03685, EA235_09845, EA242_21840, EA245_13060, EA250_03470, EAM59_20420, EAN70_19975, EBM08_20240, ED600_16130, EG599_19920, EI032_11835, EIA08_14930, EKI52_25845, ELT23_21450, ELT33_08255, ELY48_05350, EPS94_00275, EPU41_11350, EQ823_15140, EQO00_10475, EWK56_23660, F7F00_18535, F7F23_18300, F7F26_19830, F9059_13225, F9X20_19985, FAF34_028090, FPI65_12170, FQU83_12075, FZN06_15895, GFU40_00265, GFU45_09775, GFU47_04605, GKE15_01895, GKE16_01895, GKE22_01895, GKE24_01895, GKE26_01895, GKE29_19115, GKE31_01895, GKE39_01895, GKE46_01895, GKE53_01895, GKE58_00135, GKE60_01895, GKE64_01895, GKE69_17480, GKE77_01900, GKE79_01895, GKE87_21705, GKE92_14745, GKE93_04890, GKE98_02435, GKF89_19095, GP666_12190, GP935_03525, GQE33_07830, GQE36_08195, GQE58_02905, GQY14_20195, HmCmsJML074_02943, HmCmsJML146_04173, NCTC10865_02596, NCTC8960_04784, NCTC9075_02775, NCTC9434_01981, RX35_00871, SAMEA3753300_03054 EC: 3.1.2
Find proteins for A0A061LQM0 (Escherichia coli) Explore A0A061LQM0  Go to UniProtKB:  A0A061LQM0

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 = 82.301	α = 90
b = 82.301	β = 90
c = 81.935	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-12 
• Released Date: 2018-10-31 
Deposition Author(s): Brett, T.J., Kober, D.L., Ohlemacher, S.I., Henderson, J.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK099534
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL119813

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