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(-) Description

Title :  NMR STRUCTURE OF THE N-TERMINAL DOMAIN A OF THE GLYCOPROTEIN CHAPERONE ERP57
 
Authors :  L. Silvennoinen, H. Tossavainen, J. Myllyharju, P. Permi
Date :  05 Aug 05  (Deposition) - 15 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Thioredoxin Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Silvennoinen, H. Tossavainen, J. Myllyharju, P. Permi
Nmr Structure Of The N-Terminal Domain A Of The Glycoprotein Chaperone Erp57
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE A3
    ChainsA
    EC Number5.3.4.1
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS
    SynonymDISULFIDE ISOMERASE ER-60, ERP60, 58 KDA MICROSOMAL PROTEIN, P58, ERP57, 58 KDA GLUCOSE REGULATED PROTEIN
    SyntheticYES

 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 2ALB)

(-) Sites  (0, 0)

(no "Site" information available for 2ALB)

(-) SS Bonds  (0, 0)

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

(-) 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, 20Tyr A:76 -Pro A:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.PDIA3_HUMAN49-67
398-416
  1A:25-43
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003002891aENSE00001489318chr15:44038590-44038904315PDIA3_HUMAN1-56561A:1-3232
1.4ENST000003002894ENSE00001782278chr15:44046022-4404610079PDIA3_HUMAN56-82271A:32-5827
1.5bENST000003002895bENSE00001672356chr15:44048847-44048964118PDIA3_HUMAN83-122401A:59-9840
1.6ENST000003002896ENSE00001792513chr15:44053622-44053729108PDIA3_HUMAN122-158371A:98-11316
1.7ENST000003002897ENSE00001692828chr15:44055275-44055404130PDIA3_HUMAN158-201440--
1.8ENST000003002898ENSE00001623236chr15:44057648-44057764117PDIA3_HUMAN201-240400--
1.9ENST000003002899ENSE00001747426chr15:44058085-44058210126PDIA3_HUMAN240-282430--
1.10ENST0000030028910ENSE00001667287chr15:44058926-44059108183PDIA3_HUMAN282-343620--
1.11bENST0000030028911bENSE00001777596chr15:44060687-44060795109PDIA3_HUMAN343-379370--
1.12ENST0000030028912ENSE00001667800chr15:44061716-44061844129PDIA3_HUMAN380-422430--
1.13aENST0000030028913aENSE00001768045chr15:44062448-4406252780PDIA3_HUMAN423-449270--
1.13cENST0000030028913cENSE00001782281chr15:44062721-4406277858PDIA3_HUMAN449-468200--
1.14bENST0000030028914bENSE00001145733chr15:44063303-440654772175PDIA3_HUMAN469-505370--

(-) 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:113
 aligned with PDIA3_HUMAN | P30101 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:113
                                    34        44        54        64        74        84        94       104       114       124       134   
          PDIA3_HUMAN    25 SDVLELTDDNFESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASV 137
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2albA00 A:1-113 Glutaredoxin                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhh......eeeeee..ee........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------THIOREDOXIN_1      ---------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-32          --------------------------Exon 1.5b  PDB: A:59-98 UniProt: 83-122 --------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.4  PDB: A:32-58     ---------------------------------------Exon 1.6         Transcript 1 (2)
                 2alb A   1 SDVLELTDDNFESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASV 113
                                    10        20        30        40        50        60        70        80        90       100       110   

   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  (0, 0)

(no "SCOP Domain" information available for 2ALB)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

NMR Structure(hide GO term definitions)
Chain A   (PDIA3_HUMAN | P30101)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    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:0004629    phospholipase C activity    Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate.
    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.
biological process
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    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:2001238    positive regulation of extrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    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:0034975    protein folding in endoplasmic reticulum    A protein folding process that takes place in the endoplasmic reticulum (ER). Secreted, plasma membrane and organelle proteins are folded in the ER, assisted by chaperones and foldases (protein disulphide isomerases), and additional factors required for optimal folding (ATP, Ca2+ and an oxidizing environment to allow disulfide bond formation).
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0006621    protein retention in ER lumen    The retention in the endoplasmic reticulum (ER) lumen of soluble resident proteins. Sorting receptors retrieve proteins with ER localization signals, such as KDEL and HDEL sequences or some transmembrane domains, that have escaped to the cis-Golgi network and return them to the ER. Abnormally folded proteins and unassembled subunits are also selectively retained in the ER.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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: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:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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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    Tyr A:76 - Pro A:77   [ RasMol ]  
 

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        PDIA3_HUMAN | P301012dmm 2h8l 3f8u

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6308