5MC3

Crystal Structure of Glu412Lys mutant of Human Prolidase with Mn ions and GlyPro ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.131 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for prolidase deficiency disease mechanisms.

Wilk, P.Uehlein, M.Piwowarczyk, R.Dobbek, H.Mueller, U.Weiss, M.S.

(2018) FEBS J 285: 3422-3441

  • DOI: https://doi.org/10.1111/febs.14620
  • Primary Citation of Related Structures:  
    5MBY, 5MBZ, 5MC0, 5MC1, 5MC2, 5MC3, 5MC4, 5MC5, 6H2P, 6H2Q

  • PubMed Abstract: 

    Prolidase is a metallopeptidase that cleaves iminodipeptides containing a proline (Pro) or hydroxyproline (Hyp) residue at their C-terminal end. The disease prolidase deficiency (PD) is a rare recessive human disorder characterized by reduced prolidase activity. PD manifests itself by a wide range of severe clinical symptoms, most commonly as skin ulceration, recurrent infections of the respiratory tract, and mental retardation. Several mutations in the PEPD gene have been identified that are responsible for the loss or the reduction of prolidase activity. In contrast, the structural basis of enzyme inactivation has so far remained elusive. In this study, we present high resolution crystal structures of a number of human prolidase (HsProl) variants, in which single amino acids are either substituted by others or deleted. The observed implications of the mutations on the three-dimensional structure of HsProl are reported and discussed and related to their enzymatic activity. The resulting structures may be divided into four groups depending on the presumed effect of the corresponding mutations on the reaction mechanism. The four possible inactivation mechanisms, which could be elucidated, are disruption of the catalytic Mn 2 (OH - )-center, introduction of chain disorder along with the displacement of important active site residues, rigidification of the active site, and flexibilization of the active site. All refined structure coordinates as well as the corresponding structure factor amplitudes have been deposited in the PDB under the accession numbers 5MBY, 5MBZ, 5MC0, 5MC1, 5MC2, 5MC3, 5MC4, 5MC5, 6H2P, 6H2Q.


  • Organizational Affiliation

    Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX), Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xaa-Pro dipeptidase
A, B
484Homo sapiensMutation(s): 1 
Gene Names: PEPDPRD
EC: 3.4.13.9
UniProt & NIH Common Fund Data Resources
Find proteins for P12955 (Homo sapiens)
Explore P12955 
Go to UniProtKB:  P12955
PHAROS:  P12955
GTEx:  ENSG00000124299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12955
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRO
Query on PRO

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
Q [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
OH
Query on OH

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.131 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.59α = 90
b = 106.412β = 90
c = 217.434γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description