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(-) Description

Title :  SOLUTION STRUCTURE OF A NOVEL BETA-GRASP FOLD LIKE DOMAIN OF HYPOTHETICAL PROTEIN (ARABIDOPSIS THALIANA)
 
Authors :  X. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 May 04  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta-Grasp Fold Like Domain, Arabidopsis Thaliana, Hypothetical Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of A Novel Beta-Grasp Fold Like Domain Of Hypothetical Protein (Arabidopsis Thaliana)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NPL4 FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030212-84
    Expression System Vector Type: PLASMID
    Fragment: HYPOTHETICAL DOMAIN
    Gene: RIKEN RAFL09-18-B15
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL 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 1WF9)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:107
 aligned with NPL41_ARATH | Q9LYC2 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:110
                                                                                                                                 96       
                                  1                                                                                            95 |       
                                  |  4        14        24        34        44        54        64        74        84        94| |    103
          NPL41_ARATH     - ------MTMLRVRSRDGLERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYEGERTIRG-GPAVTPAG 103
               SCOP domains -------d1wf9a1 A:8-101 NPL4-like protein 1                                                           --------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------UN_NPL4-1wf9A01 A:8-94                                                                 ---------------- Pfam domains
         Sec.struct. author .......eeeeee....eeeeee.....hhhhhhhhhhhhh...........hhhhhh..hhhhhh..........hhhhh......eee...............---.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1wf9 A   1 GSSGSSGTMLRVRSRDGLERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYEGERTIRGSGPS---SG 107
                                    10        20        30        40        50        60        70        80        90       100    |  107
                                                                                                                                  105 106
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  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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WF9)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (NPL41_ARATH | Q9LYC2)
molecular function
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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