3IRP

Crystal structure of functional region of UafA from Staphylococcus saprophyticus at 1.50 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb3IRP/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-24 Released: 2010-09-08 
• Deposition Author(s): Tanaka, Y., Shouji, Y., Matsuoka, E., Kuroda, M., Tanaka, I., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding

Matsuoka, E., Tanaka, Y., Kuroda, M., Shouji, Y., Ohta, T., Tanaka, I., Yao, M.

(2011) Protein Sci 20: 406-416

• PubMed: 21280131 
• DOI: https://doi.org/10.1002/pro.573
• Primary Citation of Related Structures:  
  3IRP, 3IRZ, 3IS1


• PubMed Abstract: 
  

  Staphylococci use cell wall-anchored proteins as adhesins to attach to host tissues. Staphylococcus saprophyticus, a uropathogenic species, has a unique cell wall-anchored protein, uro-adherence factor A (UafA), which shows erythrocyte binding activity. To investigate the mechanism of adhesion by UafA, we determined the crystal structure of the functional region of UafA at 1.5 Å resolution. The structure was composed of three domains, designated as the N2, N3, and B domains, arranged in a triangular relative configuration. Hemagglutination inhibition assay with domain-truncated mutants indicated that both N and B domains were necessary for erythrocyte binding. Based on these results, a novel manner of ligand binding in which the B domain acts as a functional domain was proposed as the adhesion mechanism of S. saprophyticus.

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Organizational Affiliation: 

Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.04 kDa 
• Atom Count: 3,863 
• Modelled Residue Count: 418 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uro-adherence factor A	A [auth X]	429	Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292	Mutation(s): 0  Gene Names: uafA, SSP0135
UniProt
Find proteins for Q4A0V8 (Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41)) Explore Q4A0V8  Go to UniProtKB:  Q4A0V8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth X], C [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	D [auth X], E [auth X], F [auth X], G [auth X], H [auth X]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.935	α = 90
b = 126.926	β = 96.75
c = 45.83	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Tanaka, Y., Shouji, Y., Matsuoka, E., Kuroda, M., Tanaka, I., Yao, M.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-23
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description