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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE GM2- ACTIVATOR PROTEIN
 
Authors :  C. S. Wright, L. Z. Mi, S. Lee, F. Rastinejad
Date :  26 Jul 05  (Deposition) - 25 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Constricted Lipid Binding Pocket, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. S. Wright, L. Z. Mi, S. Lee, F. Rastinejad
Crystal Structure Analysis Of Phosphatidylcholine-Gm2-Activator Product Complexes: Evidence For Hydrolase Activity.
Biochemistry V. 44 13510 2005
PubMed-ID: 16216074  |  Reference-DOI: 10.1021/BI050668W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GANGLIOSIDE GM2 ACTIVATOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneGM2A
    OrganBRAIN, KIDNEY, LIVER
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymGM2-AP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1DAO2Ligand/IonLAURIC ACID
2MYR1Ligand/IonMYRISTIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:121 , LEU A:126BINDING SITE FOR RESIDUE MYR A 3045
2AC2SOFTWAREILE A:22 , LEU A:72 , GLY A:73 , TRP A:131 , ILE A:139 , LEU A:159BINDING SITE FOR RESIDUE DAO A 2055
3AC3SOFTWARESER A:141 , LEU A:143 , GLY A:151BINDING SITE FOR RESIDUE DAO A 2057

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:152
2A:68 -A:75
3A:81 -A:107
4A:94 -A:105

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gln A:23 -Pro A:24
2Asp A:25 -Pro A:26
3Val A:29 -Pro A:30
4Ala A:47 -Pro A:48
5Glu A:96 -Pro A:97
6Cys A:107 -Pro A:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AGC)

(-) 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:162
 aligned with SAP3_MOUSE | Q60648 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:162
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SAP3_MOUSE    32 GGFSWDNCDEGKDPAVIKSLTIQPDPIVVPGDVVVSLEGKTSVPLTAPQKVELTVEKEVAGFWVKIPCVEQLGSCSYENICDLIDEYIPPGESCPEPLHTYGLPCHCPFKEGTYSLPTSNFTVPDLELPSWLSTGNYRIQSILSSGGKRLGCIKIAASLKGR 193
               SCOP domains d2agca_ A: Ganglioside M2 (gm2) activator                                                                                                                          SCOP domains
               CATH domains 2agcA00 A:1-162  [code=2.70.220.10, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.hhhh..eeeeeeeee........eeeeeeeeee........eeeeeeeeee..eeee..........ee.hhhhhhhhhh.......................eeeeeeeeeee............eeeeeeeeeee..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2agc A   1 GGFSWDNCDEGKDPAVIKSLTIQPDPIVVPGDVVVSLEGKTSVPLTAPQKVELTVEKEVAGFWVKIPCVEQLGSCSYENICDLIDEYIPPGESCPEPLHTYGLPCHCPFKEGTYSLPTSNFTVPDLELPSWLSTGNYRIQSILSSGGKRLGCIKIAASLKGR 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AGC)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SAP3_MOUSE | Q60648)
molecular function
    GO:0032428    beta-N-acetylgalactosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-beta-D-galactosaminides.
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0016787    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.
    GO:0005319    lipid transporter activity    Enables the directed movement of lipids into, out of or within a cell, or between cells.
    GO:0016004    phospholipase activator activity    Increases the activity of a phospholipase, an enzyme that catalyzes of the hydrolysis of a glycerophospholipid.
biological process
    GO:0006689    ganglioside catabolic process    The chemical reactions and pathways resulting in the breakdown of ganglioside, a ceramide oligosaccharide carrying, in addition to other sugar residues, one or more sialic residues.
    GO:0001573    ganglioside metabolic process    The chemical reactions and pathways involving ceramide oligosaccharides carrying in addition to other sugar residues, one or more sialic acid residues.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0019915    lipid storage    The accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0050877    nervous system process    A organ system process carried out by any of the organs or tissues of neurological system.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0009313    oligosaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0051345    positive regulation of hydrolase activity    Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
    GO:0006665    sphingolipid metabolic process    The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
cellular component
    GO:0045179    apical cortex    The region that lies just beneath the plasma membrane on the apical edge of a cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005889    hydrogen:potassium-exchanging ATPase complex    A protein complex that possesses hydrogen:potassium-exchanging ATPase activity; characterized in animal cells, where it maintains ionic gradients of K+ at the expense of ATP hydrolysis; The complex contains two obligatory subunits, the catalytic alpha subunit and a glycosylated beta subunit; two additional subunits, gamma and channel-inducing factor (CHIF), may also be present.
    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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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1g13 HUMAN APO-GM2AP STRUCTURE