5NYY

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

• PDB DOI: https://doi.org/10.2210/pdb5NYY/pdb

• Classification: TRANSFERASE
• Organism(s): Thermomonospora curvata DSM 43183
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-12 Released: 2017-06-07 
• Deposition Author(s): Meury, M., Knop, M., Seebeck, F.P.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.167 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Starting Model: experimental

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

• PubMed: 28544744 
• DOI: https://doi.org/10.1002/anie.201702901
• Primary Citation of Related Structures:  
  5NXL, 5NYY


• 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 Ag ^I or Cd ^II 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 Cu ^I/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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.69 kDa 
• Atom Count: 2,638 
• Modelled Residue Count: 281 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-specific serine/threonine protein kinase	A	300	Thermomonospora curvata DSM 43183	Mutation(s): 0  Gene Names: Tcur_4811 EC: 2.7.11.1 (PDB Primary Data), 1.8.3.7 (UniProt)
UniProt
Find proteins for D1A7C3 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A7C3  Go to UniProtKB:  D1A7C3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	D [auth A], E [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CD	B [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.167 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.314	α = 90
b = 67.648	β = 90
c = 100.021	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Meury, M., Knop, M., Seebeck, F.P.

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Funding Organization	Location	Grant Number
European Research Council		336559

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Advisory, Author supporting evidence, Data collection, Database references, Refinement description