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(-) Description

Title :  THE SOLUTION STRUCTURE OF THE SECOND THIOREDOXIN DOMAIN OF MOUSE PROTEIN DISULFIDE-ISOMERASE A4
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 30 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein Erp-72, Erp72, Cai, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Second Thioredoxin Domain Of Mouse Protein Disulfide-Isomerase A4
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE A4
    Chains: A
    EC Number: 5.3.4.1
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050425-14
    Expression System Vector Type: PLASMID
    Fragment: 2ND THIOREDOXIN DOMAIN
    Gene: PDIA4, CAI, ERP72
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: PROTEIN ERP-72, ERP72

 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 2DJ2)

(-) Sites  (0, 0)

(no "Site" information available for 2DJ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DJ2)

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ser A:57 -Pro A:58
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:82 -Pro A:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DJ2)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.PDIA4_MOUSE76-94
191-209
540-558		  1-
A:28-46
-
2THIOREDOXIN_2PS51352 Thioredoxin domain profile.PDIA4_MOUSE162-294
16-160
498-629		  1A:8-118
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2DJ2)

(-) 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:120
 aligned with PDIA4_MOUSE | P08003 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:152
                                                                                                                                                                279                 
                                                                                                                                                              278 |                 
                                   155       165       175       185       195       205       215       225       235       245       255       265       275  | |  284       294  
          PDIA4_MOUSE   146 GSRTQEEIVAKVREVSQPDWTPPPEVTLSLTKDNFDDVVNNADIILVEFYAPWCGHCKKLAPEYEKAAKELSKRSPPIPLAKVDATEQTDLAKRFDVSGYPTLKIFRKGRPFDYNGPREKYGIVDYMIEQSGP-PSKEILTLKQVQEFLKDG 296
               SCOP domains d2                  dj2a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------.................hhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhh......eeeee....eee.....hhhhhhhhhhhhhhh...--------------.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  ------------------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------THIOREDOXIN_2  PDB: A:8-118 UniProt: 162-294                                                                                          -- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dj2 A   1 GS------------------SGSSGVTLSLTKDNFDDVVNNADIILVEFYAPWCGHCKKLAPEYEKAAKELSKRSPPIPLAKVDATEQTDLAKRFDVSGYPTLKIFRKGRPFDYNGPREKYGIVDYMIEQSGSGPS--------------SG 120
                             |       -         -|       12        22        32        42        52        62        72        82        92       102       112     |   -         -| 
                             2                  3                                                                                                                118            119
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DJ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DJ2)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (PDIA4_MOUSE | P08003)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0034663    endoplasmic reticulum chaperone complex    A protein complex that is located in the endoplasmic reticulum and is composed of chaperone proteins, including BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.

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    Ser A:57 - Pro A:58   [ RasMol ]  
    Tyr A:82 - Pro A:83   [ RasMol ]  
 

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 Related Entries

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        PDIA4_MOUSE | P08003: 2dj1 2dj3

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