7QZH

SFX structure of dye-type peroxidase DtpB D152A variant in the ferric state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB.

Lucic, M.Wilson, M.T.Tosha, T.Sugimoto, H.Shilova, A.Axford, D.Owen, R.L.Hough, M.A.Worrall, J.A.R.

(2022) ACS Catal 12: 13349-13359

  • DOI: https://doi.org/10.1021/acscatal.2c03754
  • Primary Citation of Related Structures:  
    7QZE, 7QZF, 7QZG, 7QZH, 7ZMJ

  • PubMed Abstract: 

    Controlling the reactivity of high-valent Fe(IV)-O catalytic intermediates, Compounds I and II, generated in heme enzymes upon reaction with dioxygen or hydrogen peroxide, is important for function. It has been hypothesized that the presence (wet) or absence (dry) of distal heme pocket water molecules can influence whether Compound I undergoes sequential one-electron additions or a concerted two-electron reduction. To test this hypothesis, we investigate the role of water in the heme distal pocket of a dye-decolorizing peroxidase utilizing a combination of serial femtosecond crystallography and rapid kinetic studies. In a dry distal heme site, Compound I reduction proceeds through a mechanism in which Compound II concentration is low. This reaction shows a strong deuterium isotope effect, indicating that reduction is coupled to proton uptake. The resulting protonated Compound II (Fe(IV)-OH) rapidly reduces to the ferric state, giving the appearance of a two-electron transfer process. In a wet site, reduction of Compound I is faster, has no deuterium effect, and yields highly populated Compound II, which is subsequently reduced to the ferric form. This work provides a definitive experimental test of the hypothesis advanced in the literature that relates sequential or concerted electron transfer to Compound I in wet or dry distal heme sites.


  • Organizational Affiliation

    School of Life Sciences, University of Essex, Wivenhoe Park, Essex, ColchesterCO4 3SQ, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dyp-type peroxidase family
A, B, C, D, E
A, B, C, D, E, F
316Streptomyces lividansMutation(s): 1 
Gene Names: SSPG_00656
UniProt
Find proteins for A0A7U8UU09 (Streptomyces lividans TK24)
Explore A0A7U8UU09 
Go to UniProtKB:  A0A7U8UU09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U8UU09
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
J [auth C]
K [auth D]
M [auth E]
G [auth A],
I [auth B],
J [auth C],
K [auth D],
M [auth E],
N [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.5α = 90
b = 121.1β = 90
c = 198γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R021015/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description