3UI5

Crystal structure of human Parvulin 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.096 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic proof for an extended hydrogen-bonding network in small prolyl isomerases.

Mueller, J.W.Link, N.M.Matena, A.Hoppstock, L.Ruppel, A.Bayer, P.Blankenfeldt, W.

(2011) J.Am.Chem.Soc. 133: 20096-20099

  • DOI: 10.1021/ja2086195
  • Primary Citation of Related Structures:  3UI4

  • PubMed Abstract: 
  • Parvulins compose a family of small peptidyl-prolyl isomerases (PPIases) involved in protein folding and protein quality control. A number of amino acids in the catalytic cavity are highly conserved, but their precise role within the catalytic mechan ...

    Parvulins compose a family of small peptidyl-prolyl isomerases (PPIases) involved in protein folding and protein quality control. A number of amino acids in the catalytic cavity are highly conserved, but their precise role within the catalytic mechanism is unknown. The 0.8 Å crystal structure of the prolyl isomerase domain of parvulin Par14 shows the electron density of hydrogen atoms between the D74, H42, H123, and T118 side chains. This threonine residue has previously not been associated with catalysis, but a corresponding T152A mutant of Pin1 shows a dramatic reduction of catalytic activity without compromising protein stability. The observed catalytic tetrad is strikingly conserved in Pin1- and parvulin-type proteins and hence constitutes a common feature of small peptidyl prolyl isomerases.


    Organizational Affiliation

    Institute for Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4
A
101Homo sapiensGene Names: PIN4
EC: 5.2.1.8
Find proteins for Q9Y237 (Homo sapiens)
Go to Gene View: PIN4
Go to UniProtKB:  Q9Y237
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
D1D
Query on D1D

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Download CCD File 
A
(4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.096 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.170α = 90.00
b = 47.060β = 90.00
c = 51.830γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-12-05
    Type: Structure summary
  • Version 1.2: 2013-01-09
    Type: Database references