5EQ3

Crystal structure of the SrpA adhesin from Streptococcus sanguinis with a sialyl galactose disaccharide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin.

Bensing, B.A.Loukachevitch, L.V.McCulloch, K.M.Yu, H.Vann, K.R.Wawrzak, Z.Anderson, S.Chen, X.Sullam, P.M.Iverson, T.M.

(2016) J.Biol.Chem. 291: 7230-7240

  • DOI: 10.1074/jbc.M115.701425
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Streptococcus sanguinisis a leading cause of infective endocarditis, a life-threatening infection of the cardiovascular system. An important interaction in the pathogenesis of infective endocarditis is attachment of the organisms to host platelets.S. ...

    Streptococcus sanguinisis a leading cause of infective endocarditis, a life-threatening infection of the cardiovascular system. An important interaction in the pathogenesis of infective endocarditis is attachment of the organisms to host platelets.S. sanguinisexpresses a serine-rich repeat adhesin, SrpA, similar in sequence to platelet-binding adhesins associated with increased virulence in this disease. In this study, we determined the first crystal structure of the putative binding region of SrpA (SrpABR) both unliganded and in complex with a synthetic disaccharide ligand at 1.8 and 2.0 Å resolution, respectively. We identified a conserved Thr-Arg motif that orients the sialic acid moiety and is required for binding to platelet monolayers. Furthermore, we propose that sequence insertions in closely related family members contribute to the modulation of structural and functional properties, including the quaternary structure, the tertiary structure, and the ligand-binding site.


    Organizational Affiliation

    From the Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco and the Northern California Institute for Research and Education, San Francisco, California 94121.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet-binding glycoprotein
A, B
201Streptococcus sanguinis (strain SK36)Mutation(s): 0 
Gene Names: srpA
Find proteins for A3CM52 (Streptococcus sanguinis (strain SK36))
Go to UniProtKB:  A3CM52
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGC
Query on NGC

Download SDF File 
Download CCD File 
A
3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
N-glycolylneuraminic acid
C11 H19 N O10
FDJKUWYYUZCUJX-VTERZIIISA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MBG
Query on MBG

Download SDF File 
Download CCD File 
A
METHYL-BETA-GALACTOSE
C7 H14 O6
HOVAGTYPODGVJG-VOQCIKJUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 174.620α = 90.00
b = 47.005β = 102.15
c = 64.026γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI106987
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI41513
Department of Veteran's AffairsUnited States--
American Heart AssociationUnited States14GRNT20390021
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008320
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesT32 HL007751
National Institutes of Health/National Center for Research ResourcesUnited StatesS10 RR026915
Department of Energy (United States)United StatesDE-AC02-06CH11357
Michigan Economic Development CorporationUnited States085P1000817

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations