7M7A | pdb_00007m7a

Legionella pneumophila MavQ lipid kinase

PDB DOI: https://doi.org/10.2210/pdb7M7A/pdb

Classification: TRANSFERASE
Organism(s): Legionella pneumophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-27 Released: 2021-04-28
Deposition Author(s): Tomchick, D.R., Tagliabracci, V.S., Hsieh, T.S., Lopez, V.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/Office of the Director, Robert A. Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), National Center for Research and Development (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.283 (Depositor), 0.278 (DCC)
R-Value Work:
0.239 (Depositor), 0.238 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Dynamic remodeling of host membranes by self-organizing bacterial effectors.

Hsieh, T.S., Lopez, V.A., Black, M.H., Osinski, A., Pawlowski, K., Tomchick, D.R., Liou, J., Tagliabracci, V.S.

(2021) Science 372: 935-941

PubMed: 33927055 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.aay8118
Primary Citation Related Structures:
7M7A

PubMed Abstract:
During infection, intracellular bacterial pathogens translocate a variety of effectors into host cells that modify host membrane trafficking for their benefit. We found a self-organizing system consisting of a bacterial phosphoinositide kinase and its opposing phosphatase that formed spatiotemporal patterns, including traveling waves, to remodel host cellular membranes. The Legionella effector MavQ, a phosphatidylinositol (PI) 3-kinase, was targeted to the endoplasmic reticulum (ER). MavQ and the Legionella PI 3-phosphatase SidP, even in the absence of other bacterial components, drove rapid PI 3-phosphate turnover on the ER and spontaneously formed traveling waves that spread along ER subdomains inducing vesicle and tubule budding. Thus, bacteria can exploit a self-organizing membrane-targeting mechanism to hijack host cellular structures for survival.

Organizational Affiliation

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecule Content

Total Structure Weight: 275.72 kDa
Atom Count: 17,652
Modeled Residue Count: 2,125
Deposited Residue Count: 2,360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoinositide 3-kinase MavQ	A, B, C, D	590	Legionella pneumophila	Mutation(s): 0 Gene Names: lpg2975 EC: 3.1.3.64
UniProt
Find proteins for Q5ZRA8 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRA8 Go to UniProtKB: Q5ZRA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZRA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.283 (Depositor), 0.278 (DCC)
R-Value Work: 0.239 (Depositor), 0.238 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.399	α = 90
b = 210.235	β = 90
c = 499.861	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PDB_EXTRACT	data extraction
SHELXD	phasing
MLPHARE	phasing
PARROT	phasing
BUCCANEER	model building
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM137419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM113079
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008203-29
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	F30HL143859-01
National Institutes of Health/Office of the Director	United States	S10OD025018
Robert A. Welch Foundation	United States	I-1911
Robert A. Welch Foundation	United States	I-1789
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP170674
National Center for Research and Development (Poland)	Poland	PPN/BEK/2018/1/00431
National Institutes of Health/Office of the Director	United States	S10OD021685