1M22

X-ray structure of native peptide amidase from Stenotrophomonas maltophilia at 1.4 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An alternative mechanism for amidase signature enzymes

Labahn, J.Neumann, S.Buldt, G.Kula, M.-R.Granzin, J.

(2002) J Mol Biol 322: 1053-1064

  • DOI: 10.1016/s0022-2836(02)00886-0
  • Primary Citation of Related Structures:  
    1M22, 1M21

  • PubMed Abstract: 
  • The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide ...

    The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide amidase (Pam) interesting for different biotechnological applications. Pam belongs to the amidase signature (AS) family. It is the first protein within this family whose tertiary structure has been solved. The structure of the native Pam has been determined with a resolution of 1.4A and in complex with the competitive inhibitor chymostatin at a resolution of 1.8A. Chymostatin, which forms acyl adducts with many serine proteases, binds non-covalently to this enzyme.Pam folds as a very compact single-domain protein. The AS sequence represents a core domain that is covered by alpha-helices. This AS domain contains the catalytic residues. It is topologically homologous to the phosphoinositol phosphatase domain. The structural data do not support the recently proposed Ser-Lys catalytic dyad mechanism for AS enzymes. Our results are in agreement with the role of Ser226 as the primary nucleophile but differ concerning the roles of Ser202 and Lys123: Ser202, with direct contact both to the substrate molecule and to Ser226, presumably serves as an acid/bases catalyst. Lys123, with direct contact to Ser202 but no contact to Ser226 or the substrate molecule, most likely acts as an acid catalyst.


    Related Citations: 
    • Crystallization and preliminary X-ray data of the recombinant peptide amidase from Stenotrophomonas maltophilia
      Neumann, S., Granzin, J., Kula, M.-R., Labahn, J.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 333
    • Purification and characterisation of a newly screened microbial peptide amidase
      Stelkes-Ritter, U., Wyzgol, K., Kula, M.-R.
      (1995) Appl Microbiol Biotechnol 44: 393

    Organizational Affiliation

    Forschungszentrum Jülich Gmbh, Institut für Biologische Informationsverarbeitung, IBI-2, Structural Biology, D-52425 Jülich, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
peptide amidaseAB503Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: pamDM611_04005
EC: 3.5.1
Find proteins for Q8RJN5 (Stenotrophomonas maltophilia)
Explore Q8RJN5 
Go to UniProtKB:  Q8RJN5
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.179α = 90
b = 62.596β = 90
c = 101.906γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-16
    Changes: Advisory, Data collection, Derived calculations, Refinement description