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(-) Description

Title :  SOLUTION STRUCTURE OF DC1 DOMAIN OF PDI-LIKE HYPOTHETICAL PROTEIN FROM ARABIDOPSIS THALIANA
 
Authors :  K. Miyamoto, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Nov 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dc1 Domain, Zinc Binding Domain, Pdi-Like Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miyamoto, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of Dc1 Domain Of Pdi-Like Hypothetical Protein From Arabidopsis Thaliana
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PDI-LIKE HYPOTHETICAL PROTEIN AT1G60420
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030421-05
    Expression System Vector Type: PLASMID
    Fragment: DC1 DOMAIN
    Gene: RIKEN CDNA RAFL09-40-E23
    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  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:50 , CYS A:53 , HIS A:72 , CYS A:75BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS A:35 , HIS A:38 , CYS A:64 , CYS A:67BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V5N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V5N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V5N)

(-) Exons   (0, 0)

(no "Exon" information available for 1V5N)

(-) 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:89
 aligned with NRX1_ARATH | O80763 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:120
                                   457       467       477       487       497       507       517       527       537       547       557       567
           NRX1_ARATH   448 AALGPTGQTVTKEARDLVVAHGADAYPFTEERLKEIEAKYDEIAKDWPKKVKHVLHEEHELELTRVQVYTCDKCEEEGTIWSYHCDECDFDLHAKCALNEDTKENGDEAVKVGGDESKDG 567
               SCOP domains d1v5na_                      A: Pdi-like hypothetical protein At1g60420                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------C1_3-1v5nA01 A:48-76         ----------------------- Pfam domains
         Sec.struct. author .......---------------------.....hhhhhhhhhhh.....ee..hhh....eeee.................eeee....eee.hhhhh........----------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v5n A   1 GSSGSSG---------------------TEERLKEIEAKYDEIAKDWPKKVKHVLHEEHELELTRVQVYTCDKCEEEGTIWSYHCDECDFDLHAKCALNEDTKESG----------PSSG  89
                                  |  -         -        |9        19        29        39        49        59        69        79     |   -      | 89
                                  7                     8                                                                           85         86
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V5N)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: C1 (13)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (NRX1_ARATH | O80763)
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:0047134    protein-disulfide reductase activity    Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0009860    pollen tube growth    Growth of pollen via tip extension of the intine wall.
    GO:0010183    pollen tube guidance    The process in which the growth of pollen tube is directed towards the female gametophyte.
    GO:0080092    regulation of pollen tube growth    Any process that modulates the frequency, rate or extent of pollen tube growth.
    GO:0046686    response to cadmium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
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.

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  1v5n
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