3TBE

The crystal structure of the complex of Streptococcus agalactiae sortase C1 and MTSET


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The Crystal Structure Analysis of Group B Streptococcus Sortase C1: A Model for the "Lid" Movement upon Substrate Binding.

Khare, B.Fu, Z.Q.Huang, I.H.Ton-That, H.Narayana, S.V.

(2011) J Mol Biol 414: 563-577

  • DOI: https://doi.org/10.1016/j.jmb.2011.10.017
  • Primary Citation of Related Structures:  
    3TB7, 3TBE

  • PubMed Abstract: 

    A unique feature of the class-C-type sortases, enzymes essential for Gram-positive pilus biogenesis, is the presence of a flexible "lid" anchored in the active site. However, the mechanistic details of the "lid" displacement, suggested to be a critical prelude for enzyme catalysis, are not yet known. This is partly due to the absence of enzyme-substrate and enzyme-inhibitor complex crystal structures. We have recently described the crystal structures of the Streptococcus agalactiae SAG2603 V/R sortase SrtC1 in two space groups (type II and type III) and that of its "lid" mutant and proposed a role of the "lid" as a protector of the active-site hydrophobic environment. Here, we report the crystal structures of SAG2603 V/R sortase C1 in a different space group (type I) and that of its complex with a small-molecule cysteine protease inhibitor. We observe that the catalytic Cys residue is covalently linked to the small-molecule inhibitor without lid displacement. However, the type I structure provides a view of the sortase SrtC1 lid displacement while having structural elements similar to a substrate sorting motif suitably positioned in the active site. We propose that these major conformational changes seen in the presence of a substrate mimic in the active site may represent universal features of class C sortase substrate recognition and enzyme activation.


  • Organizational Affiliation

    Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sortase family protein
A, B, C, D, E
A, B, C, D, E, F
230Streptococcus agalactiae serogroup VMutation(s): 0 
Gene Names: SAG0647
EC: 3.4.22
UniProt
Find proteins for Q8E0S7 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Go to UniProtKB:  Q8E0S7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ETM
Query on ETM

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
L [auth C]
N [auth D]
P [auth E]
G [auth A],
H [auth B],
L [auth C],
N [auth D],
P [auth E],
Q [auth F]
2-(TRIMETHYLAMMONIUM)ETHYL THIOL
C5 H14 N S
VFUGTBZQGUVGEX-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
M [auth C],
O [auth D],
R [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.41α = 90
b = 70.65β = 90.43
c = 194.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
CNSrefinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2011-10-26 
  • Deposition Author(s): Khare, B.

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Database references
  • Version 1.2: 2011-12-21
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description