3PSQ | pdb_00003psq

Crystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus biogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus assembly

Kang, H.J.Coulibaly, F.Proft, T.Baker, E.N.

(2011) PLoS One 6: e15969-e15969

  • DOI: https://doi.org/10.1371/journal.pone.0015969
  • Primary Citation Related Structures: 
    3PSQ

  • PubMed Abstract: 

    Sortase enzymes are cysteine transpeptidases that mediate the covalent attachment of substrate proteins to the cell walls of gram-positive bacteria, and thereby play a crucial role in virulence, infection and colonisation by pathogens. Many cell-surface proteins are anchored by the housekeeping sortase SrtA but other more specialised sortases exist that attach sub-sets of proteins or function in pilus assembly. The sortase Spy0129, or SrtC1, from the M1 SF370 strain of Streptococcus pyogenes is responsible for generating the covalent linkages between the pilin subunits in the pili of this organism. The crystal structure of Spy0129 has been determined at 2.3 Å resolution (R = 20.4%, Rfree  = 26.0%). The structure shows that Spy0129 is a class B sortase, in contrast to other characterised pilin polymerases, which belong to class C. Spy0129 lacks a flap believed to function in substrate recognition in class C enzymes and instead has an elaborated β6/β7 loop. The two independent Spy0129 molecules in the crystal show differences in the positions and orientations of the catalytic Cys and His residues, Cys221 and His126, correlated with movements of the β7/β8 and β4/β5 loops that respectively follow these residues. Bound zinc ions stabilise these alternative conformations in the crystal. This conformational variability is likely to be important for function although there is no evidence that zinc is involved in vivo.


  • Organizational Affiliation
    • Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 49.02 kDa 
  • Atom Count: 3,331 
  • Modeled Residue Count: 368 
  • Deposited Residue Count: 412 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical exported protein
A, B
206Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: SPy_0129
UniProt
Find proteins for Q9A1S1 (Streptococcus pyogenes serotype M1)
Explore Q9A1S1 
Go to UniProtKB:  Q9A1S1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A1S1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY

Query on ACY



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
T [auth B],
U [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.511α = 90
b = 94.511β = 90
c = 253.519γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-11-04
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations