Crystal structure of human glutaminyl cyclase in complex with N-acetylhistamine

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.199 

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Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation

Huang, K.F.Liu, Y.L.Cheng, W.J.Ko, T.P.Wang, A.H.

(2005) Proc Natl Acad Sci U S A 102: 13117-13122

  • DOI: https://doi.org/10.1073/pnas.0504184102
  • Primary Citation of Related Structures:  
    2AFM, 2AFO, 2AFS, 2AFU, 2AFW, 2AFX, 2AFZ

  • PubMed Abstract: 

    N-terminal pyroglutamate (pGlu) formation from its glutaminyl (or glutamyl) precursor is required in the maturation of numerous bioactive peptides. The aberrant formation of pGlu may be related to several pathological processes, such as osteoporosis and amyloidotic diseases. This N-terminal cyclization reaction, once thought to proceed spontaneously, is greatly facilitated by the enzyme glutaminyl cyclase (QC). To probe this important but poorly understood modification, we present here the structure of human QC in free form and bound to a substrate and three imidazole-derived inhibitors. The structure reveals an alpha/beta scaffold akin to that of two-zinc exopeptidases but with several insertions and deletions, particularly in the active-site region. The relatively closed active site displays alternate conformations due to the different indole orientations of Trp-207, resulting in two substrate (glutamine t-butyl ester)-binding modes. The single zinc ion in the active site is coordinated to three conserved residues and one water molecule, which is replaced by an imidazole nitrogen upon binding of the inhibitors. Together with structural and kinetic analyses of several active-site-mutant enzymes, a catalysis mechanism of the formation of protein N-terminal pGlu is proposed. Our results provide a structural basis for the rational design of inhibitors against QC-associated disorders.

  • Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaminyl-peptide cyclotransferase
A, B
329Homo sapiensMutation(s): 0 
Gene Names: QPCT
UniProt & NIH Common Fund Data Resources
Find proteins for Q16769 (Homo sapiens)
Explore Q16769 
Go to UniProtKB:  Q16769
PHAROS:  Q16769
GTEx:  ENSG00000115828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16769
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.199 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.132α = 90
b = 119.132β = 90
c = 332.826γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations