5SY9

Atomic resolution structure of E15Q mutant human DJ-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

Lin, J.Pozharski, E.Wilson, M.A.

(2017) Biochemistry 56: 391-402

  • DOI: 10.1021/acs.biochem.6b00906
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LB ...

    Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.


    Organizational Affiliation

    Department of Biochemistry and Redox Biology Center, University of Nebraska , Lincoln, Nebraska 68588, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein deglycase DJ-1
A
192Homo sapiensMutation(s): 1 
Gene Names: PARK7
EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q99497 (Homo sapiens)
Go to Gene View: PARK7
Go to UniProtKB:  Q99497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.118 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 86.276α = 90.00
b = 121.963β = 90.00
c = 43.512γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-10 
  • Released Date: 2016-12-28 
  • Deposition Author(s): Wilson, M.A., Lin, J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM092999

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references
  • Version 1.2: 2017-02-01
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence