1GE7

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.

Hori, T.Kumasaka, T.Yamamoto, M.Nonaka, N.Tanaka, N.Hashimoto, Y.Ueki, U.Takio, K.

(2001) Acta Crystallogr.,Sect.D 57: 361-368

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architect ...

    Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins. His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. A Tyr133 side chain located on the S1' pocket had different configurations in two crystal forms and was not observed in the other crystal forms. The flexible Tyr133 plays two roles in the enzymatic function of GfMEP. The first is to provide a hydrophobic environment with Phe83 in order to accommodate the alkyl part of the Lys side chain of a substrate and the second is as a 'proton donor' to the oxyanion of the tetrahedral transition state to stabilize the reaction transition state.


    Organizational Affiliation

    RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki, Sayo-gun 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-LYS METALLOENDOPEPTIDASE
A, B
167Grifola frondosaMutation(s): 0 
Gene Names: MEP
EC: 3.4.24.20
Find proteins for P81054 (Grifola frondosa)
Go to UniProtKB:  P81054
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 30.202α = 90.00
b = 30.202β = 90.00
c = 308.049γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata collection
CNSrefinement
PROCESSdata reduction
PROCESSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description