6KOY

Crystal structure of two domain M1 Zinc metallopeptidase E323A mutant bound to L-tryptophan amino acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.ijbiomac.2019.12.239
  • Primary Citation of Related Structures:  
    6KOY, 6KP0, 6KOZ, 6IFF

  • 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 Dein ...

    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. Electronic address: ravimakde@rrcat.gov.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc metalloproteaseAB474Deinococcus radiodurans R1Mutation(s): 1 
Gene Names: DR_0875
EC: 3.4.11.2
Find proteins for Q9RVZ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RVZ5 
Go to UniProtKB:  Q9RVZ5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download CCD File 
A, B
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.833α = 89.754
b = 57.457β = 82.636
c = 69.492γ = 67.928
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references