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(-) Description

Title :  SOLUTION STRUCTURE OF CI-MPR DOMAIN 5 BOUND TO N-ACETYLGLUCOSAMINYL 6-PHOSPHOMETHYLMANNOSIDE
 
Authors :  L. J. Olson, F. C. Peterson, B. F. Volkman, N. M. Dahms
Date :  10 Mar 10  (Deposition) - 07 Jul 10  (Release) - 25 Dec 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Transport, Lysosome, Mannose, Receptor, Sugar Binding, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Disulfide Bond, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Olson, F. C. Peterson, A. Castonguay, R. N. Bohnsack, M. Kudo, R. R. Gotschall, W. M. Canfield, B. F. Volkman, N. M. Dahms
Structural Basis For Recognition Of Phosphodiester-Containing Lysosomal Enzymes By The Cation-Independent Mannose 6-Phosphate Receptor.
Proc. Natl. Acad. Sci. Usa V. 107 12493 2010
PubMed-ID: 20615935  |  Reference-DOI: 10.1073/PNAS.1004232107

(-) Compounds

Molecule 1 - CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZ-ALPHA-A
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentCI-MPR_DOMAIN5
    GeneIGF2R, M6P
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymCI MAN-6-P RECEPTOR, CI-MPR, M6PR, INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR, INSULIN-LIKE GROWTH FACTOR II RECEPTOR, IGF-II RECEPTOR, 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR, MPR 300

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KVB)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:592 -A:628
2A:636 -A:643
3A:695 -A:724

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KVB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KVB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KVB)

(-) Sequences/Alignments

NMR Structure
   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:148
 aligned with MPRI_BOVIN | P08169 from UniProtKB/Swiss-Prot  Length:2499

    Alignment length:148
                                   631       641       651       661       671       681       691       701       711       721       731       741       751       761        
           MPRI_BOVIN   622 TAAACVLSRTEGDNCTVFDSQAGFSFDLTPLTKKDAYKVETDKYEFHINVCGPVSVGACPPDSGACQVSRSDRKSWNLGRSNAKLSYYDGMIQLTYRDGTPYNNEKRTPRATLITFLCDRDAGVGFPEYQEEDNSTYNFRWYTSYACP 769
               SCOP domains d2kvba_ A: Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------CIMR-2kvbA01 A:684-725                     Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------CIMR-2kvbA02 A:684-725                     Pfam domains (2)
         Sec.struct. author ........eee....eeee....eeee.........eeee...eeeee................eeeee.....eee.......eeee..eeeee....ee.......eeeeeeeeee.......eeeeeee...eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kvb A 578 EAEAEFLSRTEGDNCTVFDSQAGFSFDLTPLTKKDAYKVETDKYEFHINVCGPVSVGACPPDSGACQVSRSDRKSWNLGRSNAKLSYYDGMIQLTYRDGTPYNNEKRTPRATLITFLCDRDAGVGFPEYQEEDNSTYNFRWYTSYACP 725
                                   587       597       607       617       627       637       647       657       667       677       687       697       707       717        

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KVB)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: M6PR (17)
(-)
Family: CIMR (8)
1aCIMR-2kvbA01A:684-725
1bCIMR-2kvbA02A:684-725

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (MPRI_BOVIN | P08169)
molecular function
    GO:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    GO:0036143    kringle domain binding    Interacting selectively and non-covalently with a kringle domain. Kringle domains are protein domains that fold into large loops stabilized by 3 disulfide linkages, and are important in protein-protein interactions with blood coagulation factors.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MPRI_BOVIN | P081691q25 1syo 1sz0 2kva

(-) Related Entries Specified in the PDB File

2kva RELATED ID: 16773 RELATED DB: BMRB