8HI7

Crystal structure of a holoenzyme TglHI with two Fe irons for Pseudomonas syringae Peptidyl (S) 2-mercaptoglycine biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis.

Zheng, Y.Xu, X.Fu, X.Zhou, X.Dou, C.Yu, Y.Yan, W.Yang, J.Xiao, M.van der Donk, W.A.Zhu, X.Cheng, W.

(2023) Structure 31: 1220-1232.e5

  • DOI: https://doi.org/10.1016/j.str.2023.08.004
  • Primary Citation of Related Structures:  
    8HCI, 8HI7, 8HI8

  • PubMed Abstract: 

    Structural diverse natural products like ribosomally synthesized and posttranslationally modified peptides (RiPPs) display a wide range of biological activities. Currently, the mechanism of an uncommon reaction step during the biosynthesis of 3-thiaglutamate (3-thiaGlu) is poorly understood. The removal of the β-carbon from the Cys in the TglA-Cys peptide catalyzed by the TglHI holoenzyme remains elusive. Here, we present three crystal structures of TglHI complexes with and without bound iron, which reveal that the catalytic pocket is formed by the interaction of TglH-TglI and that its activation is conformation dependent. Biochemical assays suggest a minimum of two iron ions in the active cluster, and we identify the position of a third iron site. Collectively, our study offers insights into the activation and catalysis mechanisms of the non-heme dioxygen-dependent holoenzyme TglHI. Additionally, it highlights the evolutionary and structural conservation in the DUF692 family of biosynthetic enzymes that produce diverse RiPPs.


  • Organizational Affiliation

    Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RiPP Recognition protein269Pseudomonas syringae pv. maculicola str. ES4326Mutation(s): 0 
Gene Names: PMA4326_007960
UniProt
Find proteins for A0A8T8BZN3 (Pseudomonas syringae pv. maculicola str. ES4326)
Explore A0A8T8BZN3 
Go to UniProtKB:  A0A8T8BZN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8T8BZN3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF692 family protein304Pseudomonas syringae pv. maculicola str. ES4326Mutation(s): 0 
Gene Names: PMA4326_007955
UniProt
Find proteins for A0A8T8BZJ9 (Pseudomonas syringae pv. maculicola str. ES4326)
Explore A0A8T8BZJ9 
Go to UniProtKB:  A0A8T8BZJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8T8BZJ9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.63α = 90
b = 117.63β = 90
c = 86.763γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81930125

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references