4EVU

Crystal structure of C-terminal domain of putative periplasmic protein ydgH from S. enterica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO.

Eletsky, A.Michalska, K.Houliston, S.Zhang, Q.Daily, M.D.Xu, X.Cui, H.Yee, A.Lemak, A.Wu, B.Garcia, M.Burnet, M.C.Meyer, K.M.Aryal, U.K.Sanchez, O.Ansong, C.Xiao, R.Acton, T.B.Adkins, J.N.Montelione, G.T.Joachimiak, A.Arrowsmith, C.H.Savchenko, A.Szyperski, T.Cort, J.R.

(2014) Plos One 9: e101787-e101787

  • DOI: 10.1371/journal.pone.0101787
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or th ...

    Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21-91), and the C-terminal domain III (residues 244-314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed α+β fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.


    Organizational Affiliation

    Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York, United States of America; Northeast Structural Genomics Consortium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative periplasmic protein ydgH
A, B
72Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: ydgH
Find proteins for Q8ZPL1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZPL1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 39.079α = 90.00
b = 52.521β = 109.38
c = 39.139γ = 90.00
Software Package:
Software NamePurpose
SBC-Collectdata collection
DMmodel building
REFMACrefinement
HKL-3000data scaling
DMphasing
ARP/wARPmodel building
Cootmodel building
SHELXmodel building
HKL-3000data reduction
MLPHAREphasing
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references