4X36

Crystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4

  • Classification: HYDROLASE
  • Organism(s): Streptococcus pneumoniae TIGR4
  • Expression System: Escherichia coli BL21
  • Mutation(s): No 

  • Deposited: 2014-11-28 Released: 2015-05-27 
  • Deposition Author(s): Cheng, W., Li, Q., Zhou, C.Z., Chen, Y.X.
  • Funding Organization(s): Ministry of Science and Technology of China, National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, Program for Changjiang Scholars and Innovative Research Team in University

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Full-length structure of the major autolysin LytA.

Li, Q.Cheng, W.Morlot, C.Bai, X.H.Jiang, Y.L.Wang, W.Roper, D.I.Vernet, T.Dong, Y.H.Chen, Y.Zhou, C.Z.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1373-1381

  • DOI: https://doi.org/10.1107/S1399004715007403
  • Primary Citation of Related Structures:  
    4X36

  • PubMed Abstract: 

    LytA is responsible for the autolysis of many Streptococcus species, including pathogens such as S. pneumoniae, S. pseudopneumoniae and S. mitis. However, how this major autolysin achieves full activity remains unknown. Here, the full-length structure of the S. pneumoniae LytA dimer is reported at 2.1 Å resolution. Each subunit has an N-terminal amidase domain and a C-terminal choline-binding domain consisting of six choline-binding repeats, which form five canonical and one single-layered choline-binding sites. Site-directed mutageneses combined with enzymatic activity assays indicate that dimerization and binding to choline are two independent requirements for the autolytic activity of LytA in vivo. Altogether, it is suggested that dimerization and full occupancy of all choline-binding sites through binding to choline-containing TA chains enable LytA to adopt a fully active conformation which allows the amidase domain to cleave two lactyl-amide bonds located about 103 Å apart on the peptidoglycan.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autolysin318Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: lytASP_1937
EC: 3.5.1.28
UniProt
Find proteins for P06653 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P06653 
Go to UniProtKB:  P06653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06653
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHT
Query on CHT

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.282α = 90
b = 101.282β = 90
c = 119.577γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2013CB835300 and 2014CB910100
National Natural Science Foundation of ChinaChina31270781 and U1332114
Fundamental Research Funds for the Central UniversitiesChina--
Program for Changjiang Scholars and Innovative Research Team in UniversityChina--

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary