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(-) Description

Title :  CRYSTAL STRUCTURE OF THE Y137S MUTANT OF 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 :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Conformational Changes In Mobile Loop (W131 Loop), 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, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET16B (NOVAGEN)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneGM2A
    MutationYES
    OrganLIVER, BRAIN, NEURONS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGM2-AP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1IPA14Ligand/IonISOPROPYL ALCOHOL
2MYR1Ligand/IonMYRISTIC ACID
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1IPA10Ligand/IonISOPROPYL ALCOHOL
2MYR-1Ligand/IonMYRISTIC ACID
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1IPA4Ligand/IonISOPROPYL ALCOHOL
2MYR1Ligand/IonMYRISTIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:98 , LEU B:118 , HOH B:3087BINDING SITE FOR RESIDUE MYR B 3045
2AC2SOFTWAREGLU B:113BINDING SITE FOR RESIDUE IPA B 1504
3AC3SOFTWAREPHE A:82BINDING SITE FOR RESIDUE IPA A 1505
4AC4SOFTWAREGLY B:41 , SER B:42BINDING SITE FOR RESIDUE IPA B 1506
5AC5SOFTWARELEU B:100 , PRO B:106BINDING SITE FOR RESIDUE IPA B 1511
6AC6SOFTWAREHOH A:1611BINDING SITE FOR RESIDUE IPA A 1513
7AC7SOFTWAREHOH A:1657BINDING SITE FOR RESIDUE IPA A 1514
8AC8SOFTWAREPRO A:97 , GLU A:98 , IPA A:1517BINDING SITE FOR RESIDUE IPA A 1515
9AC9SOFTWAREPRO A:97 , IPA A:1515BINDING SITE FOR RESIDUE IPA A 1517

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:10 -A:154
2A:70 -A:77
3A:83 -A:109
4A:96 -A:107

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Glu A:25 -Pro A:26
2Asp A:27 -Pro A:28
3Val A:31 -Pro A:32
4Ser A:49 -Pro A:50
5Glu A:98 -Pro A:99
6Cys A:109 -Pro A:110
7Glu B:25 -Pro B:26
8Asp B:27 -Pro B:28
9Val B:31 -Pro B:32
10Ser B:49 -Pro B:50
11Glu B:98 -Pro B:99
12Cys B:109 -Pro B:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036892I59VSAP3_HUMANPolymorphism153477A/BV30V
2UniProtVAR_036893M69VSAP3_HUMANPolymorphism153478A/BV40V
3UniProtVAR_006947C138RSAP3_HUMANDisease (GM2GAB)137852797A/BC109R
4UniProtVAR_011698R169PSAP3_HUMANDisease (GM2GAB)104893892A/BR140P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036892I59VSAP3_HUMANPolymorphism153477AV30V
2UniProtVAR_036893M69VSAP3_HUMANPolymorphism153478AV40V
3UniProtVAR_006947C138RSAP3_HUMANDisease (GM2GAB)137852797AC109R
4UniProtVAR_011698R169PSAP3_HUMANDisease (GM2GAB)104893892AR140P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036892I59VSAP3_HUMANPolymorphism153477BV30V
2UniProtVAR_036893M69VSAP3_HUMANPolymorphism153478BV40V
3UniProtVAR_006947C138RSAP3_HUMANDisease (GM2GAB)137852797BC109R
4UniProtVAR_011698R169PSAP3_HUMANDisease (GM2GAB)104893892BR140P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AG9)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003571643ENSE00001085753chr5:150632453-150632858406SAP3_HUMAN1-27270--
1.4aENST000003571644aENSE00001328369chr5:150639316-150639477162SAP3_HUMAN28-81542A:1-52
B:1-52
52
52
1.5bENST000003571645bENSE00001085757chr5:150646292-150646474183SAP3_HUMAN82-142612A:53-113
B:53-113
61
61
1.6ENST000003571646ENSE00001427604chr5:150646857-1506500013145SAP3_HUMAN143-193512A:114-164
B:114-164
51
51

(-) Sequences/Alignments

Asymmetric 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:164
 aligned with SAP3_HUMAN | P17900 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:164
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189    
           SAP3_HUMAN    30 QLSSFSWDNCDEGKDPAVIRSLTLEPDPIIVPGNVTLSVMGSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEHFCDVLDMLIPTGEPCPEPLRTYGLPCHCPFKEGTYSLPKSEFVVPDLELPSWLTTGNYRIESVLSSSGKRLGCIKIAASLKGI 193
               SCOP domains d2ag9a_ A: Ganglioside M2 (gm2) activator                                                                                                                            SCOP domains
               CATH domains 2ag9A00 A:1-164  [code=2.70.220.10, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.......eeeeeeeee........eeeeeeeeee........eeeeeeeee....eee..........ee.hhhhhhhhhh.........hhhhh.........eeeeeeeeeee.............eeeeeeeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------V---------V--------------------------------------------------------------------R------------------------------P------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4a  PDB: A:1-52 UniProt: 28-81 [INCOMPLETE]  Exon 1.5b  PDB: A:53-113 UniProt: 82-142                     Exon 1.6  PDB: A:114-164 UniProt: 143-193           Transcript 1
                 2ag9 A   1 HMSSFSWDNCDEGKDPAVIRSLTLEPDPIVVPGNVTLSVVGSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEHFCDVLDMLIPTGEPCPEPLRTYGLPCHCPFKEGTYSLPKSEFVVPDLELPSWLTTGNSRIESVLSSSGKRLGCIKIAASLKGI 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with SAP3_HUMAN | P17900 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:164
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189    
           SAP3_HUMAN    30 QLSSFSWDNCDEGKDPAVIRSLTLEPDPIIVPGNVTLSVMGSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEHFCDVLDMLIPTGEPCPEPLRTYGLPCHCPFKEGTYSLPKSEFVVPDLELPSWLTTGNYRIESVLSSSGKRLGCIKIAASLKGI 193
               SCOP domains d2ag9b_ B: Ganglioside M2 (gm2) activator                                                                                                                            SCOP domains
               CATH domains 2ag9B00 B:1-164  [code=2.70.220.10, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.......eeeeeeeee........eeeeeeeeee........eeeeeeeeee..eeeee.........ee.hhhhhhhhhh.........hhhhh.........eeeeeeeeeee..............eeeeeeeee..eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -----------------------------V---------V--------------------------------------------------------------------R------------------------------P------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4a  PDB: B:1-52 UniProt: 28-81 [INCOMPLETE]  Exon 1.5b  PDB: B:53-113 UniProt: 82-142                     Exon 1.6  PDB: B:114-164 UniProt: 143-193           Transcript 1
                 2ag9 B   1 HMSSFSWDNCDEGKDPAVIRSLTLEPDPIVVPGNVTLSVVGSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEHFCDVLDMLIPTGEPCPEPLRTYGLPCHCPFKEGTYSLPKSEFVVPDLELPSWLTTGNSRIESVLSSSGKRLGCIKIAASLKGI 164
                                    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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AG9)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SAP3_HUMAN | P17900)
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.
    GO:0030290    sphingolipid activator protein activity    Any of a group of peptide cofactors of enzymes for the lysosomal degradation of sphingolipids. They stimulate various enzymes, including glucosylceramidase, galactosylceramidase, cerebroside-sulfatase, alpha-galactosidase, beta-galactosidase, and sphingomyelin phosphodiesterase.
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:0006687    glycosphingolipid metabolic process    The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
    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:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SAP3_HUMAN | P179001g13 1pu5 1pub 1tjj 2af9 2ag2 2ag4

(-) Related Entries Specified in the PDB File

1g13 APO-PROTEIN STRUCTURE OF CRYSTALS GROWN AT PH 7.6
1pu5 PROTEIN COMPLEXED WITH GM2 GANGLIOSIDE
1pub APO-PROTEIN STRUCTURE OF CRYSTALS GROWN AT PH 5.5
1tjj PROTEIN COMPLEXED WITH PLATELET ACTIVATING FACTOR (PAF)
2ag2 PROTEIN COMPLEXED WITH PHOSPHATIDYL CHOLINE; ORTHORHOMBIC CRYSTALS
2ag4 PROTEIN COMPLEXED WITH PHOSPHATIDYL CHOLINE; MONOCLINIC CRYSTALS