2XEL | pdb_00002xel

Molecular Mechanism of Pentachloropseudilin Mediated Inhibition of Myosin Motor Activity

PDB DOI: https://doi.org/10.2210/pdb2XEL/pdb

Classification: MOTOR PROTEIN
Organism(s): Dictyostelium discoideum
Expression System: Dictyostelium discoideum
Mutation(s): No

Deposited: 2010-05-16 Released: 2011-06-15
Deposition Author(s): Chinthalapudi, K., Taft, M.H., Martin, R., Hartmann, F.K., Heissler, S.M., Tsiavaliaris, G., Gutzeit, H.O., Knoelker, H.J., Coluccio, L.M., Fedorov, R., Manstein, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.253 (Depositor), 0.249 (DCC)
R-Value Work:
0.229 (Depositor), 0.222 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanism and Specificity of Pentachloropseudilin-Mediated Inhibition of Myosin Motor Activity.

Chinthalapudi, K., Taft, M.H., Martin, R., Heissler, S.M., Preller, M., Hartmann, F.K., Brandstaetter, H., Kendrick-Jones, J., Tsiavaliaris, G., Gutzeit, H.O., Fedorov, R., Buss, F., Knoelker, H.J., Coluccio, L.M., Manstein, D.J.

(2011) J Biological Chem 286: 29700

PubMed: 21680745 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M111.239210
Primary Citation Related Structures:
2XEL

PubMed Abstract:
Here, we report that the natural compound pentachloropseudilin (PClP) acts as a reversible and allosteric inhibitor of myosin ATPase and motor activity. IC(50) values are in the range from 1 to 5 μm for mammalian class-1 myosins and greater than 90 μm for class-2 and class-5 myosins, and no inhibition was observed with class-6 and class-7 myosins. We show that in mammalian cells, PClP selectively inhibits myosin-1c function. To elucidate the structural basis for PClP-induced allosteric coupling and isoform-specific differences in the inhibitory potency of the compound, we used a multifaceted approach combining direct functional, crystallographic, and in silico modeling studies. Our results indicate that allosteric inhibition by PClP is mediated by the combined effects of global changes in protein dynamics and direct communication between the catalytic and allosteric sites via a cascade of small conformational changes along a conserved communication pathway.

Organizational Affiliation

Research Centre for Structural Analysis, Hannover Medical School, Hannover, Germany.

Macromolecule Content

Total Structure Weight: 89.4 kDa
Atom Count: 6,746
Modeled Residue Count: 776
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOSIN-2 HEAVY CHAIN	A	776	Dictyostelium discoideum	Mutation(s): 0
UniProt
Find proteins for P08799 (Dictyostelium discoideum) Explore P08799 Go to UniProtKB: P08799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08799
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AD9 Query on AD9 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADP METAVANADATE C₁₀ H₁₆ N₅ O₁₃ P₂ V XLVFTLJPBLXCED-KWIZKVQNSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
IA2 Query on IA2 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2,4-DICHLORO-6-(3,4,5-TRICHLORO-1H-PYRROL-2YL)PHENOL C₁₀ H₄ Cl₅ N O FBRLLYYPGGXCKT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253 (Depositor), 0.249 (DCC)
R-Value Work: 0.229 (Depositor), 0.222 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.53	α = 90
b = 147.49	β = 90
c = 153.78	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-15
Type: Initial release
Version 1.1: 2011-08-31
Changes: Database references, Version format compliance
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other