1GE5

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

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This is version 1.4 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 D Biol Crystallogr 57: 361-368

  • DOI: 10.1107/s0907444900019740
  • Primary Citation of Related Structures:  
    1G12, 1GE5, 1GE6, 1GE7

  • 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 architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-LYS METALLOENDOPEPTIDASEA167Grifola frondosaMutation(s): 0 
Gene Names: MEP
EC: 3.4.24.20
UniProt
Find proteins for P81054 (Grifola frondosa)
Explore P81054 
Go to UniProtKB:  P81054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81054
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download Ideal Coordinates CCD File 
B [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.8α = 105.9
b = 40.5β = 91.7
c = 30.5γ = 103.5
Software Package:
Software NamePurpose
PROCESSdata collection
PROCESSdata reduction
AMoREphasing
CNSrefinement
PROCESSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary