Structure of glycosylated glutaminyl cyclase from Drosophila melanogaster

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Crystal Structures of Glutaminyl Cyclases (QCs) from Drosophila melanogaster Reveal Active Site Conservation between Insect and Mammalian QCs.

Koch, B.Kolenko, P.Buchholz, M.Ruiz Carrillo, D.Parthier, C.Wermann, M.Rahfeld, J.U.Reuter, G.Schilling, S.Stubbs, M.T.Demuth, H.U.

(2012) Biochemistry 51: 7383-7392

  • DOI: https://doi.org/10.1021/bi300687g
  • Primary Citation of Related Structures:  
    4F9U, 4F9V, 4FAI, 4FBE

  • PubMed Abstract: 

    Glutaminyl cyclases (QCs), which catalyze the formation of pyroglutamic acid (pGlu) at the N-terminus of a variety of peptides and proteins, have attracted particular attention for their potential role in Alzheimer's disease. In a transgenic Drosophila melanogaster (Dm) fruit fly model, oral application of the potent competitive QC inhibitor PBD150 was shown to reduce the burden of pGlu-modified Aβ. In contrast to mammals such as humans and rodents, there are at least three DmQC species, one of which (isoDromeQC) is localized to mitochondria, whereas DromeQC and an isoDromeQC splice variant possess signal peptides for secretion. Here we present the recombinant expression, characterization, and crystal structure determination of mature DromeQC and isoDromeQC, revealing an overall fold similar to that of mammalian QCs. In the case of isoDromeQC, the putative extended substrate binding site might be affected by the proximity of the N-terminal residues. PBD150 inhibition of DromeQC is roughly 1 order of magnitude weaker than that of the human and murine QCs. The inhibitor binds to isoDromeQC in a fashion similar to that observed for human QCs, whereas it adopts alternative binding modes in a DromeQC variant lacking the conserved cysteines near the active center and shows a disordered dimethoxyphenyl moiety in wild-type DromeQC, providing an explanation for the lower affinity. Our biophysical and structural data suggest that isoDromeQC and human QC are similar with regard to functional aspects. The two Dm enzymes represent a suitable model for further in-depth analysis of the catalytic mechanism of animal QCs, and isoDromeQC might serve as a model system for the structure-based design of potential AD therapeutics.

  • Organizational Affiliation

    Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
312Drosophila melanogasterMutation(s): 0 
Gene Names: QCCG10487CG32412Dmel_CG32412Dmel\CG32412DromeQC
EC: (PDB Primary Data), 3.4 (PDB Primary Data)
Find proteins for Q9VRQ9 (Drosophila melanogaster)
Explore Q9VRQ9 
Go to UniProtKB:  Q9VRQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VRQ9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G94559IJ
GlyCosmos:  G94559IJ
GlyGen:  G94559IJ
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PBD PDBBind:  4F9U Ki: 944 (nM) from 1 assay(s)
Binding MOAD:  4F9U Ki: 3139 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.665α = 90
b = 56.964β = 108.16
c = 95.669γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary