5EQ4

Crystal structure of the SrpA adhesin R347E mutant from Streptococcus sanguinis

  • Classification: SUGAR BINDING PROTEIN
  • Organism(s): Streptococcus sanguinis (strain SK36)
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2015-11-12 Released: 2016-01-27 
  • Deposition Author(s): Loukachevitch, L.V., McCulloch, K.M., Vann, K.R., Wawrzak, Z., Anderson, S., Iverson, T.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; American Heart Association; Department of Veteran's Affairs; National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Heart, Lung, and Blood Institute; National Institutes of Health/National Center for Research Resources; Department of Energy (United States); Michigan Economic Development Corporation 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 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, C, D
201Streptococcus sanguinis (strain SK36)Mutation(s): 1 
Gene Names: srpA
Find proteins for A3CM52 (Streptococcus sanguinis (strain SK36))
Go to UniProtKB:  A3CM52
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 44.700α = 90.00
b = 88.055β = 90.00
c = 199.214γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

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
American Heart AssociationUnited States14GRNT 20390021
Department of Veteran's AffairsUnited States--
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: 2016-04-13
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations