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(-) Description

Title :  THE SOLUTION STRUCTURE OF THE SECOND THIOREDOXIN-LIKE DOMAIN OF HUMAN PROTEIN DISULFIDE-ISOMERASE
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 May 05  (Deposition) - 15 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dsi, Erba2L, Git, Pdi, Pdia1, Po4Db, Po4Hb, Prohb, Thioredoxin Like Domain, Redox, 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-Like Domain Of Human Protein Disulfide-Isomerase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE
    ChainsA
    EC Number5.3.4.1
    EngineeredYES
    Expression System PlasmidP040628-09
    Expression System Vector TypePLASMID
    FragmentTHIOREDOXIN LIKE DOMAIN
    GeneP4HB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPDI, PROLYL 4- HYDROXYLASE BETA SUBUNIT, CELLULAR THYROID HORMONE BINDING PROTEIN, P55

 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 1X5C)

(-) Sites  (0, 0)

(no "Site" information available for 1X5C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X5C)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:80 -Pro A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073440Y393CPDIA1_HUMANDisease (CLCRP1)786204843AY33C

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.PDIA1_HUMAN45-63
389-407
  1-
A:29-47

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003314831aENSE00001316430chr17:79818545-79818203343PDIA1_HUMAN1-49490--
1.3cENST000003314833cENSE00001326286chr17:79817263-79817057207PDIA1_HUMAN49-118700--
1.4dENST000003314834dENSE00001312577chr17:79813462-79813329134PDIA1_HUMAN118-162450--
1.5cENST000003314835cENSE00001754530chr17:79813155-79813018138PDIA1_HUMAN163-208460--
1.6bENST000003314836bENSE00001691511chr17:79805223-79805119105PDIA1_HUMAN209-243350--
1.7bENST000003314837bENSE00001800920chr17:79804948-79804823126PDIA1_HUMAN244-285420--
1.8cENST000003314838cENSE00001661432chr17:79804505-79804305201PDIA1_HUMAN286-352670--
1.9aENST000003314839aENSE00001665413chr17:79803867-79803747121PDIA1_HUMAN353-393411A:1-3333
1.9dENST000003314839dENSE00001784888chr17:79803618-79803437182PDIA1_HUMAN393-453611A:33-9361
1.10cENST0000033148310cENSE00001655750chr17:79803106-7980302087PDIA1_HUMAN454-482291A:94-12128
1.11dENST0000033148311dENSE00001594571chr17:79801968-79801037932PDIA1_HUMAN483-508260--

(-) 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:121
 aligned with PDIA1_HUMAN | P07237 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:121
                                   370       380       390       400       410       420       430       440       450       460       470       480 
          PDIA1_HUMAN   361 PEDWDKQPVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLDGFKKFLESGGQDGAGDD 481
               SCOP domains d1x5ca_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Thioredoxin-1x5cA01 A:8-113                                                                               -------- Pfam domains
         Sec.struct. author .........eee...hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee...............eeeee........ee.....hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------C---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.9a  PDB: A:1-33           ------------------------------------------------------------Exon 1.10c  PDB: A:94-121    Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.9d  PDB: A:33-93 UniProt: 393-453                     ---------------------------- Transcript 1 (2)
                 1x5c A   1 GSSGSSGPVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLDGFKKFLESGGQSGPSSG 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X5C)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (PDIA1_HUMAN | P07237)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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:0004656    procollagen-proline 4-dioxygenase activity    Catalysis of the reaction: procollagen L-proline + 2-oxoglutarate + O2 = procollagen trans-4-hydroxy-L-proline + succinate + CO2.
    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:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0042158    lipoprotein biosynthetic process    The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0018401    peptidyl-proline hydroxylation to 4-hydroxy-L-proline    The modification of peptidyl-proline to form 4-hydroxy-L-proline; catalyzed by procollagen-proline,2-oxoglutarate-4-dioxygenase.
    GO:0046598    positive regulation of viral entry into host cell    Any process that activates or increases the frequency, rate or extent of the introduction of viral entry into the host cell.
    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:1902175    regulation of oxidative stress-induced intrinsic apoptotic signaling pathway    Any process that modulates the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
    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.
    GO:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
    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:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from 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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0016222    procollagen-proline 4-dioxygenase complex    A protein complex that catalyzes the formation of procollagen trans-4-hydroxy-L-proline and succinate from procollagen L-proline and 2-oxoglutarate, requiring Fe2+ and ascorbate. Contains two alpha subunits that contribute to most parts of the catalytic sites, and two beta subunits that are identical to protein-disulfide isomerase.

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        PDIA1_HUMAN | P072371bjx 1mek 2bjx 2k18 3bj5 3uem 4ekz 4el1 4ju5

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