2IWA

Unbound glutaminyl cyclotransferase from Carica papaya.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Papaya Glutamine Cyclotransferase Shows a Singular Five-Fold Beta-Propeller Architecture that Suggests a Novel Reaction Mechanism.

Guevara, T.Mallorqui-Fernandez, N.Garcia-Castellanos, R.Garcia-Pique, S.Ebert Petersen, G.Lauritzen, C.Pedersen, J.Arnau, J.Gomis-Ruth, F.X.Sola, M.

(2006) Biol Chem 387: 1479

  • DOI: https://doi.org/10.1515/BC.2006.185
  • Primary Citation of Related Structures:  
    2IWA

  • PubMed Abstract: 

    Cyclisation of N-terminal glutamine and/or glutamate to yield pyroglutamate is an essential posttranslational event affecting a plethora of bioactive peptides and proteins. It is directly linked with pathologies ranging from neurodegenerative diseases to inflammation and several types of cancers. The reaction is catalysed by ubiquitous glutaminyl cyclotransferases (QCs), which present two distinct prototypes. Mammalian QCs are zinc-dependent enzymes with an alpha/beta-hydrolase fold. Here we present the 1.6-A-resolution structure of the other prototype, the plant analogue from Carica papaya (PQC). The hatbox-shaped molecule consists of an unusual five-fold beta-propeller traversed by a central channel, a topology that has hitherto been described only for some sugar-binding proteins and an extracellular nucleotidase. The high resistance of the enzyme to denaturation and proteolytic degradation is explained by its architecture, which is uniquely stabilised by a series of tethering elements that confer rigidity. Strikingly, the N-terminus of PQC specifically interacts with residues around the entrance to the central channel of a symmetry-related molecule, suggesting that this location is the putative active site. Cyclisation would follow a novel general-acid/base working mechanism, pivoting around a strictly conserved glutamate. This study provides a lead structure not only for plant QC orthologues, but also for bacteria, including potential human pathogens causing diphtheria, plague and malaria.


  • Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, C.S.I.C., c/ Jordi Girona, 18-26, E-08034 Barcelona, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMINE CYCLOTRANSFERASE266Carica papayaMutation(s): 0 
EC: 2.3.2.5
UniProt
Find proteins for O81226 (Carica papaya)
Explore O81226 
Go to UniProtKB:  O81226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO81226
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.74α = 90
b = 97.74β = 90
c = 64.974γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
XPREPphasing
SHELXDphasing
SHELXEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-01-30
    Changes: Database references, Derived calculations, Non-polymer description, Source and taxonomy
  • Version 1.3: 2019-04-03
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2019-05-29
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.6: 2024-11-06
    Changes: Data collection, Database references, Structure summary