3EMY

Crystal structure of Trichoderma reesei aspartic proteinase complexed with pepstatin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A.

Nascimento, A.S.Krauchenco, S.Golubev, A.M.Gustchina, A.Wlodawer, A.Polikarpov, I.

(2008) J.Mol.Biol. 382: 763-778

  • DOI: 10.1016/j.jmb.2008.07.043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 A resolution and 15. ...

    The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 A resolution and 15.8% (R(free)=19.2%) at 1.85 A resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity.


    Organizational Affiliation

    Grupo de Cristalografia, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense, 400, CEP 13560-970, São Carlos, São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trichoderma reesei Aspartic protease
A
329Hypocrea jecorinaMutation(s): 0 
Gene Names: proA
Find proteins for Q2WBH2 (Hypocrea jecorina)
Go to UniProtKB:  Q2WBH2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pepstatin
B
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000557
Query on PRD_000557
BPepstatinOligopeptide / Enzyme inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.141 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.276α = 90.00
b = 74.276β = 90.00
c = 160.027γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
PHENIXrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-02-27
    Type: Other