7ODA | pdb_00007oda

OXA-48-like Beta-lactamase OXA-436

PDB DOI: https://doi.org/10.2210/pdb7ODA/pdb

Classification: HYDROLASE
Organism(s): Enterobacter asburiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-29 Released: 2021-09-08
Deposition Author(s): Lund, B.A., Thomassen, A.M., Carlsen, T.J.W., Leiros, H.K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.227 (Depositor), 0.233 (DCC)
R-Value Work:
0.183 (Depositor), 0.195 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Biochemical and biophysical characterization of the OXA-48-like carbapenemase OXA-436.

Lund, B.A., Thomassen, A.M., Carlsen, T.J.W., Leiros, H.K.S.

(2021) Acta Crystallogr F Struct Biol Commun 77: 312-318

PubMed: 34473108 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X21008645
Primary Citation Related Structures:
7ODA

PubMed Abstract:
The crystal structure of the class D β-lactamase OXA-436 was solved to a resolution of 1.80 Å. Higher catalytic rates were found at higher temperatures for the clinically important antibiotic imipenem, indicating better adaptation of OXA-436 to its mesophilic host than OXA-48, which is believed to originate from an environmental source. Furthermore, based on the most populated conformations during 100 ns molecular-dynamics simulations, it is postulated that the modulation of activity involves conformational shifts of the α3-α4 and β5-β6 loops. While these changes overall do not cause clinically significant shifts in the resistance profile, they show that antibiotic-resistance enzymes exist in a continuum. It is believed that these seemingly neutral differences in the sequence exist on a path leading to significant changes in substrate selectivity.

Organizational Affiliation

The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.

Macromolecule Content

Total Structure Weight: 113.27 kDa
Atom Count: 9,154
Modeled Residue Count: 964
Deposited Residue Count: 976
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	244	Enterobacter asburiae	Mutation(s): 0 Gene Names: blaOXA-436 EC: 3.5.2.6
UniProt
Find proteins for A0A0S2C593 (Enterobacter asburiae) Explore A0A0S2C593 Go to UniProtKB: A0A0S2C593
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S2C593
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	G [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth C]