6VXC

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Molecular basis for catabolism of the abundant metabolitetrans-4-hydroxy-L-proline by a microbial glycyl radical enzyme.

Backman, L.R.Huang, Y.Y.Andorfer, M.C.Gold, B.Raines, R.T.Balskus, E.P.Drennan, C.L.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.51420
  • Primary Citation of Related Structures:  
    6VXC, 6VXE

  • PubMed Abstract: 

    The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans -4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to ( S )-Δ 1 -pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trans-4-hydroxy-L-proline dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H
809Clostridioides difficile 70-100-2010Mutation(s): 0 
Gene Names: pflDcsdB_2BGU81_07860BN1095_640054BN1096_740112BN1097_360077SAMEA3375004_02654
EC: 4.2.1.172
UniProt
Find proteins for Q180C6 (Clostridioides difficile (strain 630))
Explore Q180C6 
Go to UniProtKB:  Q180C6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ180C6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.346α = 90
b = 341.655β = 107.14
c = 122.605γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM126982

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description