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(-) Description

Title :  PROTEIN DISULFIDE ISOMERASE
 
Authors :  J. Kemmink, K. Dijkstra, M. Mariani, R. M. Scheek, E. Penka, M. Nilges, N. J. Darby
Date :  30 Jan 99  (Deposition) - 09 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (24x)
Keywords :  Electron Transport, Redox-Active Center, Isomerase, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kemmink, K. Dijkstra, M. Mariani, R. M. Scheek, E. Penka, M. Nilges, N. J. Darby
The Structure In Solution Of The B Domain Of Protein Disulfide Isomerase.
J. Biomol. Nmr V. 13 357 1999
PubMed-ID: 10383197  |  Reference-DOI: 10.1023/A:1008341820489
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PROTEIN DISULFIDE ISOMERASE)
    ChainsA
    EC Number5.3.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET12A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentB DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBL21 (DE3)

 Structural Features

(-) Chains, Units

  
NMR Structure (24x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2BJX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003314831aENSE00001316430chr17:79818545-79818203343PDIA1_HUMAN1-49490--
1.3cENST000003314833cENSE00001326286chr17:79817263-79817057207PDIA1_HUMAN49-118700--
1.4dENST000003314834dENSE00001312577chr17:79813462-79813329134PDIA1_HUMAN118-162451A:119-14527
1.5cENST000003314835cENSE00001754530chr17:79813155-79813018138PDIA1_HUMAN163-208461A:146-19146
1.6bENST000003314836bENSE00001691511chr17:79805223-79805119105PDIA1_HUMAN209-243351A:192-22635
1.7bENST000003314837bENSE00001800920chr17:79804948-79804823126PDIA1_HUMAN244-285421A:227-2282
1.8cENST000003314838cENSE00001661432chr17:79804505-79804305201PDIA1_HUMAN286-352670--
1.9aENST000003314839aENSE00001665413chr17:79803867-79803747121PDIA1_HUMAN353-393410--
1.9dENST000003314839dENSE00001784888chr17:79803618-79803437182PDIA1_HUMAN393-453610--
1.10cENST0000033148310cENSE00001655750chr17:79803106-7980302087PDIA1_HUMAN454-482290--
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:110
 aligned with PDIA1_HUMAN | P07237 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:110
                                   145       155       165       175       185       195       205       215       225       235       245
          PDIA1_HUMAN   136 AATTLPDGAAAESLVESSEVAVIGFFKDVESDSAKQFLQAAEAIDDIPFGITSNSDVFSKYQLDKDGVVLFKKFDEGRNNFEGEVTKENLLDFIKHNQLPLVIEFTEQTA 245
               SCOP domains d2bjxa_ A: Protein disulfide isomerase, PDI                                                                    SCOP domains
               CATH domains 2bjxA00 A:119-228 Glutaredoxin                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhh..eeeeee......hhhhhhhhhhhh....eeee....hhhhhh.....eeeeee..............hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4d  PDB: A:119-145  Exon 1.5c  PDB: A:146-191 UniProt: 163-208    Exon 1.6b  PDB: A:192-226          1. Transcript 1
                 2bjx A 119 AATTLPDGAAAESLVESSEVAVIGFFKDVESDSAKQFLQAAEAIDDIPFGITSNSDVFSKYQLDKDGVVLFKKFDEGRNNFEGEVTKENLLDFIKHNQLPLVIEFTEQTA 228
                                   128       138       148       158       168       178       188       198       208       218       228

   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  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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        PDIA1_HUMAN | P072371bjx 1mek 1x5c 2k18 3bj5 3uem 4ekz 4el1 4ju5

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