4WGF | pdb_00004wgf

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 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4WGF

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 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. m.k.groftehauge@durham.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 184.12 kDa 
  • Atom Count: 13,755 
  • Modeled Residue Count: 1,616 
  • Deposited Residue Count: 1,640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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