4EVU

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

• PDB DOI:  https://doi.org/10.2210/pdb4EVU/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-26 Released: 2012-05-30 
• Deposition Author(s): Michalska, K., Cui, H., Xu, X., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Savchenko, A., Adkins, J.N., Joachimiak, A., Program for the Characterization of Secreted Effector Proteins (PCSEP), Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.172 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 

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

• PubMed: 25010333 
• DOI: https://doi.org/10.1371/journal.pone.0101787
• Primary Citation of Related Structures:  
  2M2J, 2MA4, 2MA8, 4EVU


• 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 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.

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Organizational Affiliation: 

Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.75 kDa 
• Atom Count: 1,271 
• Modelled Residue Count: 133 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative periplasmic protein ydgH	A, B	72	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: STM1478, ydgH
UniProt
Find proteins for Q8ZPL1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPL1  Go to UniProtKB:  Q8ZPL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.172 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34EVU

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.079	α = 90
b = 52.521	β = 109.38
c = 39.139	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Michalska, K., Cui, H., Xu, X., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Savchenko, A., Adkins, J.N., Joachimiak, A., Program for the Characterization of Secreted Effector Proteins (PCSEP), Midwest Center for Structural Genomics (MCSG)

Revision History  

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