1T5E | pdb_00001t5e

The structure of MexA

PDB DOI: https://doi.org/10.2210/pdb1T5E/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2004-05-04 Released: 2004-05-18
Deposition Author(s): Higgins, M.K., Bokma, E., Koronakis, E., Hughes, C., Koronakis, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.285 (Depositor), 0.278 (DCC)
R-Value Work:
0.273 (Depositor), 0.268 (DCC)
R-Value Observed:
0.274 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structure of the periplasmic component of a bacterial drug efflux pump

Higgins, M.K., Bokma, E., Koronakis, E., Hughes, C., Koronakis, V.

(2004) Proc Natl Acad Sci U S A 101: 9994-9999

PubMed: 15226509 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0400375101
Primary Citation Related Structures:
1T5E

PubMed Abstract:
Multidrug resistance among Gram-negative bacteria is conferred by three-component membrane pumps that expel diverse antibiotics from the cell. These efflux pumps consist of an inner membrane transporter such as the AcrB proton antiporter, an outer membrane exit duct of the TolC family, and a periplasmic protein known as the adaptor. We present the x-ray structure of the MexA adaptor from the human pathogen Pseudomonas aeruginosa. The elongated molecule contains three linearly arranged subdomains; a 47-A-long alpha-helical hairpin, a lipoyl domain, and a six-stranded beta-barrel. In the crystal, hairpins of neighboring MexA monomers pack side-by-side to form twisted arcs. We discuss the implications of the packing of molecules within the crystal. On the basis of the structure and packing, we suggest a model for the key periplasmic interaction between the outer membrane channel and the adaptor protein in the assembled drug efflux pump.

Organizational Affiliation

Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom. mkh20@hermes.cam.ac.uk

Macromolecule Content

Total Structure Weight: 503.41 kDa
Atom Count: 23,101
Modeled Residue Count: 3,003
Deposited Residue Count: 4,680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug resistance protein mexA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	360	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: MEXA, PA0425 Membrane Entity: Yes
UniProt
Find proteins for P52477 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P52477 Go to UniProtKB: P52477
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52477
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth M] SDF format, chain W [auth J] SDF format, chain O [auth B] SDF format, chain N [auth A] MOL2 format, chain Z [auth M] MOL2 format, chain W [auth J] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] mmCIF format, chain Z [auth M] mmCIF format, chain W [auth J] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A]	N [auth A], O [auth B], W [auth J], Z [auth M]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth B] Focus chain W [auth J] Focus chain Z [auth M] Interactions & Density Focus chain N [auth A] Focus chain O [auth B] Focus chain W [auth J] Focus chain Z [auth M]
3GR Query on 3GR Download:Ideal Coordinates CCD File SDF format, chain Y [auth L] SDF format, chain X [auth K] SDF format, chain V [auth I] SDF format, chain U [auth H] SDF format, chain T [auth G] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth C] MOL2 format, chain Y [auth L] MOL2 format, chain X [auth K] MOL2 format, chain V [auth I] MOL2 format, chain U [auth H] MOL2 format, chain T [auth G] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] mmCIF format, chain Y [auth L] mmCIF format, chain X [auth K] mmCIF format, chain V [auth I] mmCIF format, chain U [auth H] mmCIF format, chain T [auth G] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C]	P [auth C] Q [auth D] R [auth E] S [auth F] T [auth G] P [auth C], Q [auth D], R [auth E], S [auth F], T [auth G], U [auth H], V [auth I], X [auth K], Y [auth L]	D-Glyceraldehyde C₃ H₆ O₃ MNQZXJOMYWMBOU-VKHMYHEASA-N		Interactions Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain X [auth K] Focus chain Y [auth L] Interactions & Density Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain X [auth K] Focus chain Y [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.285 (Depositor), 0.278 (DCC)
R-Value Work: 0.273 (Depositor), 0.268 (DCC)
R-Value Observed: 0.274 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.551	α = 90
b = 183.585	β = 107.38
c = 213.314	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-05-18
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-08
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-12-25
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary