› 5ctv

X-ray diffraction
1.05Å resolution

Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment

Released:
DOI: 10.2210/pdb5ctv/pdb
PDB entry 5ctv coloured by chain, front view.
PDB entry 5ctv coloured by chain, side view.
PDB entry 5ctv coloured by chain, top view.
Source organisms:
Primary publication:
The crystal structure of the major pneumococcal autolysin LytA in complex with a large peptidoglycan fragment reveals the pivotal role of glycans for lytic activity.
Sandalova T, Lee M, Henriques-Normark B, Hesek D, Mobashery S, Mellroth P, Achour A
Mol Microbiol 101 954-67 (2016)
PMID: 27273793

Function and Biology Details

Reaction catalysed: 
Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139116 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Autolysin Chain: A
Molecule details ›
Chain: A
Length: 188 amino acids
Theoretical weight: 21.2 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P06653 (Residues: 1-180; Coverage: 57%)
Gene names: SP_1937, lytA
Sequence domains: N-acetylmuramoyl-L-alanine amidase
Structure domains: Peptidoglycan recognition protein-like
fragment of peptidoglycan Chains: C, E
Molecule details ›
Chains: C, E
Length: 5 amino acids
Theoretical weight: 490 Da
Source organism: Streptococcus pneumoniae
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: AMV, NAG
Ligand AMV 2 x AMV
Ligand NAG 2 x NAG
No bound ligands
2 modified residues:
Ligand DGL 2 x DGL
Ligand DAL 4 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 44.566Å b: 54.623Å c: 78.877Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.135 0.134 0.153
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

1 review citation

Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases.
Alcorlo et al. (2017)
9 other articles

6 mentions without citation

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan.
Vermassen et al. (2019)
5 more