1M21

Crystal structure analysis of the peptide amidase PAM in complex with the competitive inhibitor chymostatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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:  
    1M21, 1M22

  • 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 amidase (Pam) interesting for different biotechnological applications ...

    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

    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 AmidaseA, B503Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: pamDM611_04005
EC: 3.5.1
UniProt
Find proteins for Q8RJN5 (Stenotrophomonas maltophilia)
Explore Q8RJN5 
Go to UniProtKB:  Q8RJN5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CHYMOSTATINC, D4Streptomyces hygroscopicusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHA
Query on PHA
C, DL-PEPTIDE LINKINGC9 H11 N OPHE
Binding Affinity Annotations 
IDSourceBinding Affinity
CHY PDBBind:  1M21 Ki: 300 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000558
Query on PRD_000558
C, DChymostatin AOligopeptide / Enzyme inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.598α = 90
b = 62.559β = 90
c = 102.382γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other