3HRT | pdb_00003hrt

Crystal Structure of ScaR with bound Cd2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.282 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.232 (DCC) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Characterization and structure of the manganese-responsive transcriptional regulator ScaR.

Stoll, K.E.Draper, W.E.Kliegman, J.I.Golynskiy, M.V.Brew-Appiah, R.A.Phillips, R.K.Brown, H.K.Breyer, W.A.Jakubovics, N.S.Jenkinson, H.F.Brennan, R.G.Cohen, S.M.Glasfeld, A.

(2009) Biochemistry 48: 10308-10320

  • DOI: https://doi.org/10.1021/bi900980g
  • Primary Citation Related Structures: 
    3HRS, 3HRT, 3HRU

  • PubMed Abstract: 

    The streptococcal coaggregation regulator (ScaR) of Streptococcus gordonii is a manganese-dependent transcriptional regulator. When intracellular manganese concentrations become elevated, ScaR represses transcription of the scaCBA operon, which encodes a manganese uptake transporter. A member of the DtxR/MntR family of metalloregulators, ScaR shares sequence similarity with other family members, and many metal-binding residues are conserved. Here, we show that ScaR is an active dimer, with two dimers binding the 46 base pair scaC operator. Each ScaR subunit binds two manganese ions, and the protein is activated by a variety of other metal ions, including Cd(2+), Co(2+), and Ni(2+) but not Zn(2+). The crystal structure of apo-ScaR reveals a tertiary and quaternary structure similar to its homologue, the iron-responsive regulator DtxR. While each DtxR subunit binds a metal ion in two sites, labeled primary and ancillary, crystal structures of ScaR determined in the presence of Cd(2+) and Zn(2+) show only a single occupied metal-binding site that is novel to ScaR. The site analogous to the primary site in DtxR is unoccupied, and the ancillary site is absent from ScaR. Instead, metal ions bind to ScaR at a site labeled "secondary", which is composed of Glu80, Cys123, His125, and Asp160 and lies roughly 5 A away from where the ancillary site would be predicted to exist. This difference suggests that ScaR and its closely related homologues are activated by a mechanism distinct from that of either DtxR or MntR.


  • Organizational Affiliation
    • Department of Chemistry, Reed College, Portland, Oregon 97202, USA.

Macromolecule Content 

  • Total Structure Weight: 49.82 kDa 
  • Atom Count: 3,411 
  • Modeled Residue Count: 419 
  • Deposited Residue Count: 428 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metalloregulator ScaR
A, B
214Streptococcus gordoniiMutation(s): 0 
Gene Names: scaR
UniProt
Find proteins for Q9RFN3 (Streptococcus gordonii)
Explore Q9RFN3 
Go to UniProtKB:  Q9RFN3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RFN3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.282 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.232 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.86α = 90
b = 70.86β = 90
c = 304.1γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description