2ZK9

Crystal Structure of Protein-glutaminase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.098 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of protein glutaminase and its pro forms converted into enzyme-substrate complex

Hashizume, R., Maki, Y., Mizutani, K., Takahashi, N., Matsubara, H., Sugita, A., Sato, K., Yamaguchi, S., Mikami, B.

(2011) J Biol Chem 286: 38691-38702

  • DOI: 10.1074/jbc.M111.255133
  • Primary Citation of Related Structures:  
    2ZK9, 3A54, 3A55, 3A56

  • PubMed Abstract: 

    • Protein glutaminase, which converts a protein glutamine residue to a glutamate residue, is expected to be useful as a new food-processing enzyme. The crystal structures of the mature and pro forms of the enzyme were refined at 1.15 and 1.73 Å resolution, respectively ...

    Protein glutaminase, which converts a protein glutamine residue to a glutamate residue, is expected to be useful as a new food-processing enzyme. The crystal structures of the mature and pro forms of the enzyme were refined at 1.15 and 1.73 Å resolution, respectively. The overall structure of the mature enzyme has a weak homology to the core domain of human transglutaminase-2. The catalytic triad (Cys-His-Asp) common to transglutaminases and cysteine proteases is located in the bottom of the active site pocket. The structure of the recombinant pro form shows that a short loop between S2 and S3 in the proregion covers and interacts with the active site of the mature region, mimicking the protein substrate of the enzyme. Ala-47 is located just above the pocket of the active site. Two mutant structures (A47Q-1 and A47Q-2) refined at 1.5 Å resolution were found to correspond to the enzyme-substrate complex and an S-acyl intermediate. Based on these structures, the catalytic mechanism of protein glutaminase is proposed.

    Organizational Affiliation: 

    Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-glutaminaseA [auth X]185Chryseobacterium proteolyticumMutation(s): 0 
Gene Names: prgA
EC: 3.5.1
UniProt
Find proteins for Q9AQQ8 (Chryseobacterium proteolyticum)
Explore Q9AQQ8 
Go to UniProtKB:  Q9AQQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AQQ8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth X]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth X]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.098 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.306α = 90
b = 62.306β = 90
c = 185.532γ = 120
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-03-13 
  • Released Date: 2009-03-17 
    • Deposition Author(s): Hashizume, R.
  • This entry supersedes: 2Z8T

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2012-08-29
    Changes: Database references, Other