6J4N

Structure of papua new guinea MBL-1(PNGM-1) native

Summary for 6J4N

• Entry DOI: 10.2210/pdb6j4n/pdb
• Descriptor: Metallo-beta-lactamases PNGM-1, ZINC ION (3 entities in total)
• Functional Keywords: metallo beta lactamse, zinc binding motif, metagenomic research, hydrolase
• Biological source: uncultured bacterium
• Total number of polymer chains: 8
• Total formula weight: 334658.73

Authors

Hong, M.K.,Park, K.S.,Jeon, J.H.,Lee, J.H.,Park, Y.S.,Lee, S.H.,Kang, L.W. (deposition date: 2019-01-10, release date: 2019-02-27, Last modification date: 2024-03-27)

Primary citation

Park, K.S.,Hong, M.K.,Jeon, J.W.,Kim, J.H.,Jeon, J.H.,Lee, J.H.,Kim, T.Y.,Karim, A.M.,Malik, S.K.,Kang, L.W.,Lee, S.H.
The novel metallo-beta-lactamase PNGM-1 from a deep-sea sediment metagenome: crystallization and X-ray crystallographic analysis.
Acta Crystallogr F Struct Biol Commun, 74:644-649, 2018

PubMed Abstract: Metallo-β-lactamases (MBLs) are present in major Gram-negative pathogens and environmental species, and pose great health risks because of their ability to hydrolyze the β-lactam rings of antibiotics such as carbapenems. PNGM-1 was the first reported case of a subclass B3 MBL protein that was identified from a metagenomic library from deep-sea sediments that predate the antibiotic era. In this study, PNGM-1 was overexpressed, purified and crystallized. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2.10 and 2.30 Å resolution, respectively. Both the native and the selenomethionine-labelled PNGM-1 crystals belonged to the monoclinic space group P2, with unit-cell parameters a = 122, b = 83, c = 163 Å, β = 110°. Matthews coefficient (V) calculations suggested the presence of 6-10 molecules in the asymmetric unit, corresponding to a solvent content of ∼31-58%. Structure determination is currently in progress.

PubMed: 30279316
DOI: 10.1107/S2053230X18012268

Experimental method

X-RAY DIFFRACTION (2.1 Å)