3PB4

Crystal structure of the catalytic domain of human Golgi-resident glutaminyl cyclase at pH 6.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of human Golgi-resident glutaminyl cyclase and its complexes with inhibitors reveal a large loop movement upon inhibitor binding

Huang, K.F.Liaw, S.S.Huang, W.L.Chia, C.Y.Lo, Y.C.Chen, Y.L.Wang, A.H.J.

(2011) J.Biol.Chem. 286: 12439-12449

  • DOI: 10.1074/jbc.M110.208595
  • Primary Citation of Related Structures:  3PB6, 3PB7, 3PB8, 3PB9, 3PBB, 3PBE

  • PubMed Abstract: 
  • Aberrant pyroglutamate formation at the N terminus of certain peptides and proteins, catalyzed by glutaminyl cyclases (QCs), is linked to some pathological conditions, such as Alzheimer disease. Recently, a glutaminyl cyclase (QC) inhibitor, PBD150, ...

    Aberrant pyroglutamate formation at the N terminus of certain peptides and proteins, catalyzed by glutaminyl cyclases (QCs), is linked to some pathological conditions, such as Alzheimer disease. Recently, a glutaminyl cyclase (QC) inhibitor, PBD150, was shown to be able to reduce the deposition of pyroglutamate-modified amyloid-β peptides in brain of transgenic mouse models of Alzheimer disease, leading to a significant improvement of learning and memory in those transgenic animals. Here, we report the 1.05-1.40 Å resolution structures, solved by the sulfur single-wavelength anomalous dispersion phasing method, of the Golgi-luminal catalytic domain of the recently identified Golgi-resident QC (gQC) and its complex with PBD150. We also describe the high-resolution structures of secretory QC (sQC)-PBD150 complex and two other gQC-inhibitor complexes. gQC structure has a scaffold similar to that of sQC but with a relatively wider and negatively charged active site, suggesting a distinct substrate specificity from sQC. Upon binding to PBD150, a large loop movement in gQC allows the inhibitor to be tightly held in its active site primarily by hydrophobic interactions. Further comparisons of the inhibitor-bound structures revealed distinct interactions of the inhibitors with gQC and sQC, which are consistent with the results from our inhibitor assays reported here. Because gQC and sQC may play different biological roles in vivo, the different inhibitor binding modes allow the design of specific inhibitors toward gQC and sQC.


    Organizational Affiliation

    Institute of Biological Chemistry, Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaminyl-peptide cyclotransferase-like protein
X
330Homo sapiensGene Names: QPCTL
EC: 2.3.2.5
Find proteins for Q9NXS2 (Homo sapiens)
Go to Gene View: QPCTL
Go to UniProtKB:  Q9NXS2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
X
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.126 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.158α = 90.00
b = 68.610β = 90.00
c = 77.410γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SHELXSphasing
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-03
    Type: Database references