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(-) Description

Title :  MP1-P14 SCAFFOLDING COMPLEX
 
Authors :  J. D. Schrag, M. Cygler, C. Munger, A. Magloire
Date :  02 Apr 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Scaffold, Complex, Alpha/Beta, Endosome, Membrane, Lysosome, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Cui, T. Sulea, J. D. Schrag, C. Munger, M. N. Hung, M. Naim, M. Cygler, E. O. Purisima
Molecular Dynamics-Solvated Interaction Energy Studies Of Protein-Protein Interactions: The Mp1-P14 Scaffolding Complex.
J. Mol. Biol. V. 379 787 2008
PubMed-ID: 18479705  |  Reference-DOI: 10.1016/J.JMB.2008.04.035
(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 Plasmid: PETDUET
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: MAP2K1IP1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Synonym: MEK-BINDING PARTNER 1, MP1
 
Molecule 2 - MITOGEN-ACTIVATED PROTEIN-BINDING PROTEIN- INTERACTING PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: MAPBPIP
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Synonym: LATE ENDOSOMAL/LYSOSOMAL MP1-INTERACTING PROTEIN, P14

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ZL1)

(-) Sites  (0, 0)

(no "Site" information available for 2ZL1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZL1)

(-) 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 2ZL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZL1)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZL1)

(-) 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:119
 aligned with LTOR3_HUMAN | Q9UHA4 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
          LTOR3_HUMAN     2 ADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV 120
               SCOP domains d2zl1a_ A: MEK binding partner 1, MP1                                                                                   SCOP domains
               CATH domains 2zl1A00 A:2-120 Dynein light chain 2a, cytoplasmic                                                                      CATH domains
               Pfam domains -MAPKK1_Int-2zl1A01 A:3-120                                                                                             Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2zl1 A   2 ADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQGSKAGASKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with LTOR2_MOUSE | Q9JHS3 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
          LTOR2_MOUSE     2 LRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEE 117
               SCOP domains d2zl1b_ B: Late endosomal/lysosomal Mp1 interacting protein p14                                                      SCOP domains
               CATH domains 2zl1B00 B:2-117 Dynein light chain 2a, cytoplasmic                                                                   CATH domains
               Pfam domains ---Robl_LC7-2zl1B01 B:5-95                                                                    ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....eeeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2zl1 B   2 LRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEE 117
                                    11        21        31        41        51        61        71        81        91       101       111
   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  (23, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LTOR3_HUMAN | Q9UHA4)
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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    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:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    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:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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: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: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 1veu 3cpt
        LTOR3_HUMAN | Q9UHA4: 1sko 3cpt

(-) Related Entries Specified in the PDB File

3cpt