Crystal structure of M1 zinc metallopeptidase E323A mutant from Deinococcus radiodurans

Experimental Data Snapshot

  • Resolution: 1.83 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase.

Agrawal, R.Goyal, V.D.Singh, R.Kumar, A.Jamdar, S.N.Kumar, A.Makde, R.D.

(2020) Int J Biol Macromol 147: 304-313

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.12.239
  • Primary Citation of Related Structures:  
    6IFF, 6KOY, 6KOZ, 6KP0, 6KP1

  • PubMed Abstract: 

    M1 metallopeptidases regulate many important biological processes such as angiogenesis, tumour growth, hormone regulation, and immune cell development. Knowledge of substrate specificity mechanism in this family is valuable. An M1 peptidase from Deinococcus radiodurans (M1dr) with preference for bulky hydrophobic residues at N-terminus of peptide substrates was recently reported. In contrast to Escherichia coli aminopeptidase N, a previously characterized M1 peptidase, M1dr exhibits reduced activity towards peptides with N-terminal Arg or Ala residue. In order to illuminate structural basis of substrate specificity, we report several crystal structures of M1dr with different amino acids bound to the active site. Structural analysis indicated that the enzyme makes subtle adjustments to multiple residues leading to significant volume change of the active site cavity to accommodate residues of varying sizes (Leu to Trp). This study further reveals that the low preference for Arg at N-terminus of peptide substrate arises from a non-productive conformation in which many of the Arg molecules bind where they block the proton donor essential for the peptidase reaction. Hence, this study illuminates the substrate-binding mechanism and also reveals the structural basis for the substrate specificity of M1dr enzyme.

  • Organizational Affiliation

    High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc metalloprotease
A, B
474Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 1 
Gene Names: DR_0875
Find proteins for Q9RVZ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RVZ5 
Go to UniProtKB:  Q9RVZ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RVZ5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.83 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.48α = 89.66
b = 57.658β = 82.07
c = 69.786γ = 67.54
Software Package:
Software NamePurpose
Cootmodel building
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2021-04-07
    Changes: Derived calculations
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description