1QWY

Latent LytM at 1.3 A resolution

Summary for 1QWY

• Entry DOI: 10.2210/pdb1qwy/pdb
• Descriptor: peptidoglycan hydrolase, ZINC ION (3 entities in total)
• Functional Keywords: lytm lysostaphin metalloprotease asparagine switch, hydrolase
• Biological source: Staphylococcus aureus subsp. aureus NCTC 8325
• Cellular location: Secreted : O33599
• Total number of polymer chains: 1
• Total formula weight: 31827.76

Authors

Odintsov, S.G.,Sabala, I.,Marcyjaniak, M.,Bochtler, M. (deposition date: 2003-09-03, release date: 2004-01-20, Last modification date: 2024-02-14)

Primary citation

Odintsov, S.G.,Sabala, I.,Marcyjaniak, M.,Bochtler, M.
Latent LytM at 1.3A resolution.
J.Mol.Biol., 335:775-785, 2004

PubMed Abstract: LytM, an autolysin from Staphylococcus aureus, is a Zn(2+)-dependent glycyl-glycine endopeptidase with a characteristic HxH motif that belongs to the lysostaphin-type (MEROPS M23/37) of metallopeptidases. Here, we present the 1.3A crystal structure of LytM, the first structure of a lysostaphin-type peptidase. In the LytM structure, the Zn(2+) is tetrahedrally coordinated by the side-chains of N117, H210, D214 and H293, the second histidine of the HxH motif. Although close to the active-site, H291, the first histidine of the HxH motif, is not directly involved in Zn(2+)-coordination, and there is no water molecule in the coordination sphere of the Zn(2+), suggesting that the crystal structure shows a latent form of the enzyme. Although LytM has not previously been considered as a proenzyme, we show that a truncated version of LytM that lacks the N-terminal part with the poorly conserved Zn(2+) ligand N117 has much higher specific activity than full-length enzyme. This observation is consistent with the known removal of profragments in other lysostaphin-type proteins and with a prior observation of an active LytM degradation fragment in S.aureus supernatant. The "asparagine switch" in LytM is analogous to the "cysteine switch" in pro-matrix metalloproteases.

PubMed: 14687573
DOI: 10.1016/j.jmb.2003.11.009

Experimental method

X-RAY DIFFRACTION (1.3 Å)