4WGF

YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.3390/ijms160715971
  • Primary Citation of Related Structures:  
    4WGF, 4WH0

  • 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 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

    School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK. [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable hydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H
205Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for Q9I4D6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4D6 
Go to UniProtKB:  Q9I4D6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4D6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HX2
Query on HX2

Download Ideal Coordinates CCD File 
DA [auth F]
IA [auth G]
J [auth A]
M [auth A]
MA [auth H]
DA [auth F],
IA [auth G],
J [auth A],
M [auth A],
MA [auth H],
O [auth B],
S [auth C],
W [auth D]
(2R,5R)-hexane-2,5-diol
C6 H14 O2
OHMBHFSEKCCCBW-PHDIDXHHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth E]
FA [auth F]
GA [auth F]
KA [auth G]
L [auth A]
BA [auth E],
FA [auth F],
GA [auth F],
KA [auth G],
L [auth A],
OA [auth H],
Q [auth B],
U [auth C],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ROP
Query on ROP

Download Ideal Coordinates CCD File 
CA [auth F]
HA [auth G]
I [auth A]
LA [auth H]
N [auth B]
CA [auth F],
HA [auth G],
I [auth A],
LA [auth H],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
PROPIONAMIDE
C3 H7 N O
QLNJFJADRCOGBJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
JA [auth G]
K [auth A]
NA [auth H]
AA [auth E],
EA [auth F],
JA [auth G],
K [auth A],
NA [auth H],
P [auth B],
T [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
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: 2.34 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.36α = 90
b = 74.48β = 92.29
c = 141.06γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary