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(-) Description

Title :  2DZJ/SOLUTION STRUCTURE OF THE N-TERMINAL UBIQUITIN-LIKE DOMAIN IN HUMAN SYNAPTIC GLYCOPROTEIN SC2
 
Authors :  C. Zhao, M. Yoneyama, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Sep 06  (Deposition) - 29 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Synaptic Glycoprotein Sc2, Ubiquitin-Like Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhao, M. Yoneyama, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
2Dzj/Solution Structure Of The N-Terminal Ubiquitin-Like Domain In Human Synaptic Glycoprotein Sc2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPTIC GLYCOPROTEIN SC2
    ChainsA
    EngineeredYES
    Expression System PlasmidP060522-14
    Expression System Vector TypePLASMID
    FragmentUBIQUITIN-LIKE DOMAIN
    GeneGPSN2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DZJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002155671ENSE00001371444chr19:14640382-14640523142TECR_HUMAN1-551A:8-125
1.3ENST000002155673ENSE00001138910chr19:14673337-1467338751TECR_HUMAN6-22171A:13-2917
1.4ENST000002155674ENSE00000655654chr19:14674018-1467406952TECR_HUMAN23-40181A:30-4718
1.5ENST000002155675ENSE00000655653chr19:14674470-1467451445TECR_HUMAN40-55161A:47-6216
1.6ENST000002155676ENSE00000655652chr19:14674612-14674715104TECR_HUMAN55-89351A:62-8827
1.7ENST000002155677ENSE00000655651chr19:14674794-14674909116TECR_HUMAN90-128390--
1.8ENST000002155678ENSE00000892876chr19:14674994-14675099106TECR_HUMAN128-163360--
1.9ENST000002155679ENSE00000655650chr19:14675598-1467567073TECR_HUMAN164-188250--
1.10ENST0000021556710ENSE00000655649chr19:14675761-1467580444TECR_HUMAN188-202150--
1.11ENST0000021556711ENSE00000655647chr19:14675878-1467593558TECR_HUMAN203-222200--
1.12ENST0000021556712ENSE00000655646chr19:14676014-1467610289TECR_HUMAN222-251300--
1.13ENST0000021556713ENSE00000655645chr19:14676430-1467647546TECR_HUMAN252-267160--
1.14bENST0000021556714bENSE00001138903chr19:14676556-14676791236TECR_HUMAN267-308420--

(-) 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:88
 aligned with TECR_HUMAN | Q9NZ01 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:88
                                   1                                                                                
                                   | 3        13        23        33        43        53        63        73        
            TECR_HUMAN    - -------MKHYEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYFRDL 81
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee.......eeeeee....hhhhhhhhhhhhh.........ee.....................eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -------1.1  Exon 1.3         Exon 1.4          --------------Exon 1.6  PDB: A:62-88      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.5        -------------------------- Transcript 1 (2)
                  2dzj A  1 GSSGSSGMKHYEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYFRDL 88
                                    10        20        30        40        50        60        70        80        

   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  (0, 0)

(no "SCOP Domain" information available for 2DZJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (TECR_HUMAN | Q9NZ01)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    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:0017099    very-long-chain-acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a very long chain fatty acid residue. A very long-chain fatty acid is a fatty acid which has a chain length greater than C22.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0030497    fatty acid elongation    The elongation of a fatty acid chain by the sequential addition of two-carbon units.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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:0035338    long-chain fatty-acyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of a long-chain fatty-acyl-CoA any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0042761    very long-chain fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid which has a chain length greater than C22.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum 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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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