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Crystal Structure of Myotubularin-related protein 2 complexed with phosphate
Biology and Chemistry Report
1LW3
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text PROTEIN-PHOSPHATE COMPLEX, HYDROLASE

    Polymeric Molecules

    Chain A
    Description Myotubularin-related protein 2 
    Fragment PH and phosphatase domains (residues 1-643) 
    Mutation C417S 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 75007.4 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    PO4  PHOSPHATE ION  O4 P   94.97  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A MTMR2_HUMAN A6NN98     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    2091   Negative Regulation of Receptor Internalization  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Receptor Internalization. 
    6470   Protein Dephosphorylation  The Process of Removing One or More Phosphoric Residues From a Protein. 
    6644   Phospholipid Metabolic Process  The Chemical Reactions and Pathways Involving Phospholipids Any Lipid Containing Phosphoric Acid As a Mono or Diester. 
    6661   Phosphatidylinositol Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Phosphatidylinositol Any Glycophospholipid in Which the Sn Glycerol 3 Phosphate Residue Is Esterified to the 1 Hydroxyl Group of 1d Myo Inositol. 
    8219   Cell Death  Any Biological Process That Results in Permanent Cessation of All Vital Functions of a Cell. a Cell Should Be Considered Dead When Any One of the Following Molecular or Morphological Criteria Is Met: (1) the Cell Has Lost the Integrity of Its Plasma Membrane; (2) the Cell Including Its Nucleus Has Undergone Complete Fragmentation Into Discrete Bodies (frequently Referred to As "apoptotic Bodies"); And/or (3) Its Corpse (or Its Fragments) Have Been Engulfed by an Adjacent Cell in Vivo. 
    16311   Dephosphorylation  The Process of Removing One or More Phosphoric (ester or Anhydride) Residues From a Molecule. 
    31642   Negative Regulation of Myelination  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Formation of a Myelin Sheath Around Nerve Axons. 
    32288   Myelin Assembly  The Process in Which the Wraps of Cell Membrane That Constitute Myelin Are Laid Down Around an Axon in the Central or Peripheral Nervous System. 
    35335   Peptidyl Tyrosine Dephosphorylation  The Removal of Phosphoric Residues From Peptidyl O Phospho Tyrosine to Form Peptidyl Tyrosine. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    45806   Negative Regulation of Endocytosis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Endocytosis. 
    46488   Phosphatidylinositol Metabolic Process  The Chemical Reactions and Pathways Involving Phosphatidylinositol Any Glycophospholipid in Which a Sn Glycerol 3 Phosphate Residue Is Esterified to the 1 Hydroxyl Group of 1d Myo Inositol. 
    46855   Inositol Phosphate Dephosphorylation  The Process of Removing a Phosphate Group From Any Mono or Polyphosphorylated Inositol. 
    46856   Phosphatidylinositol Dephosphorylation  The Process of Removing One or More Phosphate Groups From a Phosphatidylinositol. 
    48666   Neuron Development  The Process Whose Specific Outcome Is the Progression of a Neuron Over Time From Initial Commitment of the Cell to a Specific Fate to the Fully Functional Differentiated Cell. 
    51262   Protein Tetramerization  The Formation of a Protein Tetramer a Macromolecular Structure Consisting of Four Noncovalently Associated Identical or Nonidentical Subunits. 
    90394   Negative Regulation of Excitatory Postsynaptic Membrane Potential  Any Process That Prevents the Establishment or Decreases the Extent of the Excitatory Postsynaptic Potential (epsp) Which Is a Temporary Increase in Postsynaptic Potential Due to the Flow of Positively Charged Ions Into the Postsynaptic Cell. the Flow of Ions That Causes an Epsp Is an Excitatory Postsynaptic Current (epsc) and Makes It Easier For the Neuron to Fire an Action Potential. 
    97062   Dendritic Spine Maintenance  The Organization Process That Preserves a Dendritic Spine in a Stable Functional or Structural State. a Dendritic Spine Is a Specialized Protrusion From a Neuronal Dendrite and Is Involved in Synaptic Transmission. 
    2000643   Positive Regulation of Early Endosome to Late Endosome Transport  Any Process That Activates or Increases the Frequency Rate or Extent of Early Endosome to Late Endosome Transport. 
    2000645   Negative Regulation of Receptor Catabolic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Receptor Catabolic Process. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5768   Endosome  A Membrane Bounded Organelle to Which Materials Ingested by Endocytosis Are Delivered. 
    5774   Vacuolar Membrane  The Lipid Bilayer Surrounding the Vacuole and Separating Its Contents From the Cytoplasm of the Cell. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    8021   Synaptic Vesicle  A Secretory Organelle Some 50 Nm in Diameter of Presynaptic Nerve Terminals; Accumulates in High Concentrations of Neurotransmitters and Secretes These Into the Synaptic Cleft by Fusion with the 'active Zone' of the Presynaptic Plasma Membrane. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    30424   Axon  The Long Process of a Neuron That Conducts Nerve Impulses Usually Away From the Cell Body to the Terminals and Varicosities Which Are Sites of Storage and Release of Neurotransmitter. 
    30425   Dendrite  A Neuron Projection That Has a Short Tapering Often Branched Morphology Receives and Integrates Signals From Other Neurons or From Sensory Stimuli and Conducts a Nerve Impulse Towards the Axon or the Cell Body. in Most Neurons the Impulse Is Conveyed From Dendrites to Axon Via the Cell Body But in Some Types of Unipolar Neuron the Impulse Does Not Travel Via the Cell Body. 
    43197   Dendritic Spine  Protrusion From a Dendrite. Spines Are Specialised Subcellular Compartments Involved in the Synaptic Transmission. They Are Linked to the Dendritic Shaft by a Restriction. Because of Their Bulb Shape They Function As a Biochemical and an Electrical Compartment. Spine Remodeling Is Though to Be Involved in Synaptic Plasticity. 
    97060   Synaptic Membrane  A Specialized Area of Membrane On Either the Presynaptic or the Postsynaptic Side of a Synapse the Junction Between a Nerve Fiber of One Neuron and Another Neuron or Muscle Fiber or Glial Cell. 
    97481   Neuronal Postsynaptic Density  A Postsynaptic Density That Is Part of a Neuron. 
    4438   Phosphatidylinositol 3 Phosphatase Activity  Catalysis of the Reaction: 1 Phosphatidyl 1d Myo Inositol 3 Phosphate + H2o = 1 Phosphatidyl 1d Myo Inositol + Phosphate. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    8138   Protein Tyrosine/serine/threonine Phosphatase Activity  Catalysis of the Reactions: Protein Serine + H2o = Protein Serine + Phosphate; Protein Threonine Phosphate + H2o = Protein Threonine + Phosphate; and Protein Tyrosine Phosphate + H2o = Protein Tyrosine + Phosphate. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16791   Phosphatase Activity  Catalysis of the Hydrolysis of Phosphoric Monoesters Releasing Inorganic Phosphate. 
    42803   Protein Homodimerization Activity  Interacting Selectively and Non Covalently with an Identical Protein to Form a Homodimer. 
    52629   Phosphatidylinositol 3 5 Bisphosphate 3 Phosphatase Activity  Catalysis of the Reaction: 1 Phosphatidyl 1d Myo Inositol 3 5 Bisphosphate + H2o = a 1 Phosphatidyl 1d Myo Inositol 5 Phosphate + Phosphate + 2 H+. 
    52866   Phosphatidylinositol Phosphate Phosphatase Activity  Catalysis of the Reaction: Phosphatidylinositol Phosphate(n) + H2o = Phosphatidylinositol Phosphate(n 1) + Phosphate. This Reaction Is the Removal of a Phosphate Group From a Phosphatidylinositol Phosphate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene mtmr2
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q22 8898     myotubularin related protein 2 MTMR2    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs147341114 LS-SNP   dbSNP   A 90 D - > V Beta Ladder 52% (Exposed) 11 95595524
    rs142774695 LS-SNP   dbSNP   A 119 R - > GW Bend 34% (Intermediate) 11 95595438
    rs115150701 LS-SNP   dbSNP   A 121 P - > H Bend 75% (Exposed) 11 95595262
    rs138722981 LS-SNP   dbSNP   A 157 D - > A Turn 4% (Buried) 11 95591795
    rs142155860 LS-SNP   dbSNP   A 183 A - > S Helix 5% (Buried) 11 95591718
    rs186380748 LS-SNP   dbSNP   A 202 P - > A Bend 89% (Exposed) 11 95590766
    rs199736817 LS-SNP   dbSNP   A 210 D - > E Coil 42% (Exposed) 11 95590740
    rs113346250 LS-SNP   dbSNP   A 235 E - > G Coil 65% (Exposed) 11 95583864
    rs200898934 LS-SNP   dbSNP   A 298 E - > D Helix 15% (Intermediate) 11 95582937
    rs200384340 LS-SNP   dbSNP   A 340 E - > A Turn 89% (Exposed) 11 95581038
    rs200083635 LS-SNP   dbSNP   A 369 I - > T Helix 18% (Intermediate) 11 95580951
    rs114883605 LS-SNP   dbSNP   A 374 I - > T Coil 26% (Intermediate) 11 95580936
    rs148890896 LS-SNP   dbSNP   A 395 I - > F Helix 0% (Buried) 11 95578320
    rs145714734 LS-SNP   dbSNP   A 397 A - > G Helix 29% (Intermediate) 11 95578313
    rs141311831 LS-SNP   dbSNP   A 445 F - > S Helix 0% (Buried) 11 95578169
    rs146572467 LS-SNP   dbSNP   A 446 E - > K Helix 0% (Buried) 11 95578167
    rs142460913 LS-SNP   dbSNP   A 468 D - > H Coil 34% (Intermediate) 11 95574858
    rs202119906 LS-SNP   dbSNP   A 474 A - > T Turn 43% (Exposed) 11 95574840
    rs200892517 LS-SNP   dbSNP   A 501 N - > S Coil 24% (Intermediate) 11 95571349
    rs61735578 LS-SNP   dbSNP   A 502 E - > Q Helix 35% (Intermediate) 11 95571347
    rs558018 LS-SNP   dbSNP   A 545 N - > S Turn 11% (Intermediate) 11 95569448
    rs147170889 LS-SNP   dbSNP   A 556 Y - > C Turn 36% (Exposed) 11 95569415
    rs200717440 LS-SNP   dbSNP   A 565 Y - > F Coil 40% (Exposed) 11 95569388
    rs149476960 LS-SNP   dbSNP   A 581 I - > V Turn 20% (Intermediate) 11 95569341
    rs61735576 LS-SNP   dbSNP   A 586 R - > Q Coil 99% (Exposed) 11 95569325