3TRS

The crystal structure of aspergilloglutamic peptidase from Aspergillus niger


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


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Literature

The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis.

Sasaki, H.Kubota, K.Lee, W.C.Ohtsuka, J.Kojima, M.Iwata, S.Nakagawa, A.Takahashi, K.Tanokura, M.

(2012) J.Biochem. 152: 45-52

  • DOI: 10.1093/jb/mvs050

  • PubMed Abstract: 
  • Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic pep ...

    Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic peptidases, AGP is a unique two-chain enzyme with a light chain and a heavy chain bound non-covalently with each other, and thus is an interesting target for protein structure-function relationship studies. In this article, we report the crystal structure of a dimeric form of the enzyme at a resolution of 1.6 Å. This form has a unique structure in which the C-terminal region of the light chain of one of the molecules binds to the active site cleft of the other molecule like a part of a substrate. This form mimics the enzyme-activation product complex produced upon autoproteolysis, and provides a structural clue that could help to clarify the activation mechanism. This type of dimeric structure of a peptidase is here reported for the first time.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspergillopepsin-2 light chain
A, C
39Aspergillus nigerEC: 3.4.23.19
Find proteins for P24665 (Aspergillus niger)
Go to UniProtKB:  P24665
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspergillopepsin-2 heavy chain
B, D
173Aspergillus nigerEC: 3.4.23.19
Find proteins for P24665 (Aspergillus niger)
Go to UniProtKB:  P24665
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.692α = 90.00
b = 65.842β = 90.00
c = 77.391γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release