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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P14/MP1 COMPLEX AT 2.15 A RESOLUTION
 
Authors :  R. Kurzbauer, D. Teis, S. Maurer-Stroh, F. Eisenhaber, M. Hekman, G. P. Bourenkov, H. D. Bartunik, L. A. Huber, T. Clausen
Date :  05 Apr 04  (Deposition) - 03 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Profilin, Scaffold, Adaptor, Signaling Protein/Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kurzbauer, D. Teis, M. E. De Araujo, S. Maurer-Stroh, F. Eisenhaber, G. P. Bourenkov, H. D. Bartunik, M. Hekman, U. R. Rapp, L. A. Huber, T. Clausen
Crystal Structure Of The P14/Mp1 Scaffolding Complex: How A Twin Couple Attaches Mitogen- Activated Protein Kinase Signaling To Late Endosomes
Proc. Natl. Acad. Sci. Usa V. 101 10984 2004
PubMed-ID: 15263099  |  Reference-DOI: 10.1073/PNAS.0403435101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 INTERACTING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MP1, MEK BINDING PARTNER 1
 
Molecule 2 - LATE ENDOSOMAL/LYSOSOMAL MP1 INTERACTING PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: P14

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VEU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VEU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VEU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VEU)

(-) Exons   (0, 0)

(no "Exon" information available for 1VEU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:118
 aligned with LTOR3_MOUSE | O88653 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
          LTOR3_MOUSE     3 DDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDSAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELIKV 120
               SCOP domains d1veua_ A: MEK binding partner 1, MP1                                                                                  SCOP domains
               CATH domains 1veuA00 A:3-120 Dynein light chain 2a, cytoplasmic                                                                     CATH domains
               Pfam domains MAPKK1_Int-1veuA01 A:3-120                                                                                             Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhh......eeeeeee...eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1veu A   3 DDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDSAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELIKV 120
                                    12        22        32        42        52        62        72        82        92       102       112        


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with LTOR2_MOUSE | Q9JHS3 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                             1                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119    
          LTOR2_MOUSE     - -MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVA 123
               SCOP domains d1veub_ B: Late endosomal/lysosomal Mp1 interacting protein p14                                                              SCOP domains
               CATH domains 1veuB00 B:0-123 Dynein light chain 2a, cytoplasmic                                                                           CATH domains
               Pfam domains -----Robl_LC7-1veuB01 B:5-95                                                                    ---------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh....eeeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..eeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1veu B   0 GmLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILmDCmEGRVAITRVANLLLCmYAKETVGFGmLKAKAQALVQYLEEPLTQVA 123
                             |       9        19        29        39        49        59        69    |  |79        89   |    99   |   109       119    
                             |                                                                       74-MSE             93-MSE   103-MSE                
                             1-MSE                                                                      77-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PF (25)

(-) Gene Ontology  (20, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LTOR3_MOUSE | O88653)
molecular function
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0019209    kinase activator activity    Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0005515    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).
    GO:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0032008    positive regulation of TOR signaling    Any process that activates or increases the frequency, rate or extent of TOR signaling.
    GO:0032006    regulation of TOR signaling    Any process that modulates the frequency, rate or extent of TOR signaling.
cellular component
    GO:0071986    Ragulator complex    A protein complex that contains MAPKSP1 (MP1, Map2k1ip1), ROBLD3 (p14, Mapbpip), C11orf59 (p18), LAMTOR4 and LAMTOR5. The complex is anchored to lipid rafts in late endosome membranes via C11orf59, recruits mTORC1 to lysosomal membranes in amino acid signaling to mTORC1, constitutes a guanine nucleotide exchange factor (GEF) for the Rag GTPases, and is also involved in ERK/MAPK signaling.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B   (LTOR2_MOUSE | Q9JHS3)
molecular function
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005515    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).
    GO:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0032008    positive regulation of TOR signaling    Any process that activates or increases the frequency, rate or extent of TOR signaling.
cellular component
    GO:0071986    Ragulator complex    A protein complex that contains MAPKSP1 (MP1, Map2k1ip1), ROBLD3 (p14, Mapbpip), C11orf59 (p18), LAMTOR4 and LAMTOR5. The complex is anchored to lipid rafts in late endosome membranes via C11orf59, recruits mTORC1 to lysosomal membranes in amino acid signaling to mTORC1, constitutes a guanine nucleotide exchange factor (GEF) for the Rag GTPases, and is also involved in ERK/MAPK signaling.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LTOR2_MOUSE | Q9JHS3: 1sko 1szv 1vet 2zl1 3cpt
        LTOR3_MOUSE | O88653: 1vet

(-) Related Entries Specified in the PDB File

1vet THE SAME PROTEIN AT 1.9 A RESOLUTION