5XEV

Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.

Are, V.N.Jamdar, S.N.Ghosh, B.Goyal, V.D.Kumar, A.Neema, S.Gadre, R.Makde, R.D.

(2017) Proteins 85: 2239-2251

  • DOI: 10.1002/prot.25389
  • Primary Citation of Related Structures:  
    5XEV

  • PubMed Abstract: 
  • Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those ...

    Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 Å resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N-terminal domains such that their C-terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N-terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N-terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.


    Organizational Affiliation

    High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xaa-Pro dipeptidase,Peptidase-related proteinA416Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: DR_0478
EC: 3.4.13.9
Find proteins for Q9RX37 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RX37 
Go to UniProtKB:  Q9RX37
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.67α = 90
b = 91.879β = 98.78
c = 53.849γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AUTOMARdata collection
XDSdata processing
Aimlessdata scaling
AutoSolphasing
Cootmodel building
RESOLVEmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references