4WH0

YcaC from Pseudomonas aeruginosa with S-mercaptocysteine active site cysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.563 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of a Hidden Protein, YcaC, a Putative Cysteine Hydrolase from Pseudomonas aeruginosa, with and without an Acrylamide Adduct.

Grftehauge, M.K.Truan, D.Vasil, A.Denny, P.W.Vasil, M.L.Pohl, E.

(2015) Int J Mol Sci 16: 15971-15984

  • DOI: 10.3390/ijms160715971
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As part of the ongoing effort to functionally and structurally characterize virulence factors in the opportunistic pathogen Pseudomonas aeruginosa, we determined the crystal structure of YcaC co-purified with the target protein at resolutions of 2.34 ...

    As part of the ongoing effort to functionally and structurally characterize virulence factors in the opportunistic pathogen Pseudomonas aeruginosa, we determined the crystal structure of YcaC co-purified with the target protein at resolutions of 2.34 and 2.56 Å without a priori knowledge of the protein identity or experimental phases. The three-dimensional structure of YcaC adopts a well-known cysteine hydrolase fold with the putative active site residues conserved. The active site cysteine is covalently bound to propionamide in one crystal form, whereas the second form contains an S-mercaptocysteine. The precise biological function of YcaC is unknown; however, related prokaryotic proteins have functions in antibacterial resistance, siderophore production and NADH biosynthesis. Here, we show that YcaC is exceptionally well conserved across both bacterial and fungal species despite being non-ubiquitous. This suggests that whilst YcaC may not be part of an integral pathway, the function could confer a significant evolutionary advantage to microbial life.


    Organizational Affiliation

    Department of Chemistry, Durham University, Durham DH1 3LE, UK. ehmke.pohl@durham.ac.uk.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA. adriana.vasil@ucdenver.edu.,School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK. m.k.groftehauge@durham.ac.uk.,School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK. p.w.denny@durham.ac.uk.,Swiss Light Source, Paul Scherrer Institute, Villigen CH-5232, Switzerland. daphne.truan@a3.epfl.ch.,School of Medicine, Pharmacy and Health, Durham University, Stockton-on-Tees TS17 6BH, UK. p.w.denny@durham.ac.uk.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA. mike.vasil@ucdenver.edu.,School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK. ehmke.pohl@durham.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative hydrolase
A, B, C, D, E, F, G, H
205Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9I4D6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I4D6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.563 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.460α = 90.00
b = 114.530β = 91.90
c = 96.160γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHENIXmodel building
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release