Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61.91 kDa 
• Atom Count: 4636 
• Modelled Residue Count: 513 
• Deposited Residue Count: 528 
• Unique protein chains: 1

1ZSQ

Crystal Structure of MTMR2 in complex with phosphatidylinositol 3-phosphate

• DOI: 10.2210/pdb1ZSQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-05-25 Released: 2006-01-31 
• Deposition Author(s): Begley, M.J., Taylor, G.S., Brock, M.A., Ghosh, P., Woods, V.L., Dixon, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 

Literature

Molecular basis for substrate recognition by MTMR2, a myotubularin family phosphoinositide phosphatase

Begley, M.J., Taylor, G.S., Brock, M.A., Ghosh, P., Woods, V.L., Dixon, J.E.

(2006) Proc Natl Acad Sci U S A 103: 927-932

• PubMed: 16410353 
• DOI: 10.1073/pnas.0510006103
• Primary Citation of Related Structures:  
  1ZSQ, 1ZVR


• PubMed Abstract: 
  

Myotubularins, a large family of catalytically active and inactive proteins, belong to a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as physiological substrates. Here, by integrating crystallographic and deuterium-exchange mass spectrometry studies of human myotubularin-related protein-2 (MTMR2) in complex with phosphoinositides, we define the molecular basis for this unique substrate specificity. Phosphoinositide substrates bind in a pocket located on a positively charged face of the protein, suggesting an electrostatic mechanism for membrane targeting. A flexible, hydrophobic helix makes extensive interactions with the diacylglycerol moieties of substrates, explaining the specificity for membrane-bound phosphoinositides. An extensive H-bonding network and charge-charge interactions within the active site pocket determine phosphoinositide headgroup specificity. The conservation of these specificity determinants within the active, but not the inactive, myotubularins provides insight into the functional differences between the active and inactive members.

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Organizational Affiliation: 

Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myotubularin-related protein 2	A	528	Homo sapiens	Mutation(s): 1  Gene Names: MTMR2, KIAA1073 EC: 3.1.3 (PDB Primary Data), 3.1.3.95 (UniProt), 3.1.3.64 (UniProt)
Find proteins for Q13614 (Homo sapiens) Explore Q13614  Go to UniProtKB:  Q13614
NIH Common Fund Data Resources
PHAROS:  Q13614 GTEx:  ENSG00000087053

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PIB	A	2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE C17 H32 O16 P2 NKJZZWLREOAJGO-HODIZBBFSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.227	α = 90
b = 66.227	β = 90
c = 261.678	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-25 
• Released Date: 2006-01-31 
Deposition Author(s): Begley, M.J., Taylor, G.S., Brock, M.A., Ghosh, P., Woods, V.L., Dixon, J.E.

Revision History  

• Version 1.0: 2006-01-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance