7CZ9

Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Literature

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae.

Bharatham, N., Bhowmik, P., Aoki, M., Okada, U., Sharma, S., Yamashita, E., Shanbhag, A.P., Rajagopal, S., Thomas, T., Sarma, M., Narjari, R., Nagaraj, S., Ramachandran, V., Katagihallimath, N., Datta, S., Murakami, S.

(2021) Nat Commun 12: 5400-5400

  • DOI: https://doi.org/10.1038/s41467-021-25679-0
  • Primary Citation of Related Structures:  
    7CZ9

  • PubMed Abstract: 

    OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.

    • Organizational Affiliation: 

    Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka, India.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Efflux pump membrane transporter
A, B, C, D, E
A, B, C, D, E, F
1,042Klebsiella pneumoniaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for U5U6L7 (Klebsiella pneumoniae)
Explore U5U6L7 
Go to UniProtKB:  U5U6L7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5U6L7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY
Download Ideal Coordinates CCD File 
CB [auth C]
LA [auth B]
LD [auth F]
MA [auth B]
MD [auth F]
CB [auth C],
LA [auth B],
LD [auth F],
MA [auth B],
MD [auth F],
OC [auth E],
PC [auth E],
R [auth A],
WB [auth D]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LMT
Query on LMT
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AB [auth C]
AD [auth F]
BA [auth B]
BB [auth C]
BC [auth E]
AB [auth C],
AD [auth F],
BA [auth B],
BB [auth C],
BC [auth E],
BD [auth F],
CA [auth B],
CC [auth E],
CD [auth F],
DA [auth B],
DC [auth E],
DD [auth F],
EA [auth B],
EC [auth E],
ED [auth F],
FA [auth B],
FC [auth E],
FD [auth F],
G [auth A],
GA [auth B],
GC [auth E],
GD [auth F],
H [auth A],
HA [auth B],
HC [auth E],
HD [auth F],
I [auth A],
IA [auth B],
IC [auth E],
ID [auth F],
J [auth A],
JA [auth B],
JC [auth E],
JD [auth F],
K [auth A],
KA [auth B],
KB [auth D],
KC [auth E],
KD [auth F],
L [auth A],
LB [auth D],
LC [auth E],
M [auth A],
MB [auth D],
MC [auth E],
N [auth A],
NB [auth D],
NC [auth E],
O [auth A],
OB [auth D],
P [auth A],
PB [auth D],
Q [auth A],
QA [auth C],
QB [auth D],
RA [auth C],
RB [auth D],
SA [auth C],
SB [auth D],
TA [auth C],
TB [auth D],
UA [auth C],
UB [auth D],
VA [auth C],
VB [auth D],
WA [auth C],
XA [auth C],
YA [auth C],
YC [auth F],
ZA [auth C],
ZC [auth F]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth A]
AC [auth D]
DB [auth C]
EB [auth C]
FB [auth C]
AA [auth A],
AC [auth D],
DB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
JB [auth C],
NA [auth B],
ND [auth F],
OA [auth B],
OD [auth F],
PA [auth B],
PD [auth F],
QC [auth E],
QD [auth F],
RC [auth E],
RD [auth F],
S [auth A],
SC [auth E],
T [auth A],
TC [auth E],
U [auth A],
UC [auth E],
V [auth A],
VC [auth E],
W [auth A],
WC [auth E],
X [auth A],
XB [auth D],
XC [auth E],
Y [auth A],
YB [auth D],
Z [auth A],
ZB [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.947α = 91.28
b = 128.78β = 90.01
c = 137.262γ = 103.57
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18H02386
Japan Society for the Promotion of Science (JSPS)JapanJP18H05396
Japan Society for the Promotion of Science (JSPS)JapanJP18K06079

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description