2MK5

Solution structure of a protein domain

Summary for 2MK5

• Entry DOI: 10.2210/pdb2mk5/pdb
• Related: 4OLK 4OLS
• NMR Information: BMRB: 19752
• Descriptor: Endolysin (1 entity in total)
• Functional Keywords: hydrolase
• Biological source: Staphylococcus phage GH15
• Total number of polymer chains: 1
• Total formula weight: 14048.75

Authors

Feng, Y.,Gu, J. (deposition date: 2014-01-24, release date: 2014-05-28, Last modification date: 2024-05-01)

Primary citation

Gu, J.,Feng, Y.,Feng, X.,Sun, C.,Lei, L.,Ding, W.,Niu, F.,Jiao, L.,Yang, M.,Li, Y.,Liu, X.,Song, J.,Cui, Z.,Han, D.,Du, C.,Yang, Y.,Ouyang, S.,Liu, Z.J.,Han, W.
Structural and biochemical characterization reveals LysGH15 as an unprecedented "EF-hand-like" calcium-binding phage lysin.
Plos Pathog., 10:e1004109-e1004109, 2014

PubMed Abstract: The lysin LysGH15, which is derived from the staphylococcal phage GH15, demonstrates a wide lytic spectrum and strong lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we find that the lytic activity of the full-length LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, the structures of three individual domains of LysGH15 were determined. Unexpectedly, the crystal structure of the LysGH15 CHAP domain reveals an "EF-hand-like" calcium-binding site near the Cys-His-Glu-Asn quartet active site groove. To date, the calcium-binding site in the LysGH15 CHAP domain is unique among homologous proteins, and it represents the first reported calcium-binding site in the CHAP family. More importantly, the calcium ion plays an important role as a switch that modulates the CHAP domain between the active and inactive states. Structure-guided mutagenesis of the amidase-2 domain reveals that both the zinc ion and E282 are required in catalysis and enable us to propose a catalytic mechanism. Nuclear magnetic resonance (NMR) spectroscopy and titration-guided mutagenesis identify residues (e.g., N404, Y406, G407, and T408) in the SH3b domain that are involved in the interactions with the substrate. To the best of our knowledge, our results constitute the first structural information on the biochemical features of a staphylococcal phage lysin and represent a pivotal step forward in understanding this type of lysin.

PubMed: 24831957
DOI: 10.1371/journal.ppat.1004109

Experimental method

SOLUTION NMR