4NTE

Crystal structure of DepH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products

Scharf, D.H.Groll, M.Habel, A.Heinekamp, T.Hertweck, C.Brakhage, A.A.Huber, E.M.

(2014) Angew.Chem.Int.Ed.Engl. 53: 2221-2224

  • DOI: 10.1002/anie.201309302
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nature provides a rich source of compounds with diverse chemical structures and biological activities, among them, sulfur-containing metabolites from bacteria and fungi. Some of these compounds bear a disulfide moiety that is indispensable for their ...

    Nature provides a rich source of compounds with diverse chemical structures and biological activities, among them, sulfur-containing metabolites from bacteria and fungi. Some of these compounds bear a disulfide moiety that is indispensable for their bioactivity. Specialized oxidoreductases such as GliT, HlmI, and DepH catalyze the formation of this disulfide bridge in the virulence factor gliotoxin, the antibiotic holomycin, and the anticancer drug romidepsin, respectively. We have examined all three enzymes by X-ray crystallography and activity assays. Despite their differently sized substrate binding clefts and hence, their diverse substrate preferences, a unifying reaction mechanism is proposed based on the obtained crystal structures and further supported by mutagenesis experiments.


    Organizational Affiliation

    Departments of Molecular and Applied Microbiology and Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, and Friedrich Schiller University Jena, Beutenbergstrasse 11a, 07745 Jena (Germany).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DepH
A, B
332Chromobacterium violaceumMutation(s): 0 
Gene Names: depH
Find proteins for A4ZPY8 (Chromobacterium violaceum)
Go to UniProtKB:  A4ZPY8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.220α = 90.00
b = 78.220β = 90.00
c = 188.080γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release