5NYY

Formylglycine generating enzyme from T. curvata in complex with Cd(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Copper-Oxygen Mediated C-H Bond Activation by the Formylglycine-Generating Enzyme.

Meury, M.Knop, M.Seebeck, F.P.

(2017) Angew. Chem. Int. Ed. Engl. 56: 8115-8119

  • DOI: 10.1002/anie.201702901
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The formylglycine-generating enzyme (FGE) is a unique copper protein that catalyzes oxygen-dependent C-H activation. We describe 1.66 Å- and 1.28 Å-resolution crystal structures of FGE from Thermomonospora curvata in complex with either AgI or CdII p ...

    The formylglycine-generating enzyme (FGE) is a unique copper protein that catalyzes oxygen-dependent C-H activation. We describe 1.66 Å- and 1.28 Å-resolution crystal structures of FGE from Thermomonospora curvata in complex with either AgI or CdII providing definitive evidence for a high-affinity metal-binding site in this enzyme. The structures reveal a bis-cysteine linear coordination of the monovalent metal, and tetrahedral coordination of the bivalent metal. Similar coordination changes may occur in the active enzyme as a result of CuI/II redox cycling. Complexation of copper atoms by two cysteine residues is common among copper-trafficking proteins, but is unprecedented for redox-active copper enzymes or synthetic copper catalysts.


    Organizational Affiliation

    Department for Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-specific serine/threonine protein kinase
A
300Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9)Mutation(s): 0 
EC: 1.8.3.7
Find proteins for D1A7C3 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9))
Go to UniProtKB:  D1A7C3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.314α = 90.00
b = 67.648β = 90.00
c = 100.021γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERC336559

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references