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(-) Description

Title :  SOLUTION STRUCTURE OF THE B' DOMAIN OF THERMOPHILIC FUNGAL PROTEIN DISULFIDE ISOMERASE
 
Authors :  K. Kato, Y. Yamaguchi, O. Serve
Date :  06 Oct 09  (Deposition) - 27 Oct 09  (Release) - 19 Jan 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Thioredoxin Fold, Isomerase, Disulfide Bond, Endoplasmic Reticulum, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Serve, Y. Kamiya, A. Maeno, M. Nakano, C. Murakami, H. Sasakawa, Y. Yamaguchi, T. Harada, E. Kurimoto, M. Yagi-Utsumi, T. Iguchi, K. Inaba, J. Kikuchi, O. Asami, T. Kajino, T. Oka, M. Nakasako, K. Kato
Redox-Dependent Domain Rearrangement Of Protein Disulfide Isomerase Coupled With Exposure Of Its Substrate-Binding Hydrophobic Surface
J. Mol. Biol. 2009
PubMed-ID: 19944705  |  Reference-DOI: 10.1016/J.JMB.2009.11.049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE
    Chains: A
    EC Number: 5.3.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Variant: DE3
    Expression System Vector Type: PLASMID
    Fragment: B' DOMAIN, UNP RESIDUES 228-355
    Organism Scientific: HUMICOLA INSOLENS
    Organism Taxid: 34413
    Synonym: PDI

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KP2)

(-) Sites  (0, 0)

(no "Site" information available for 2KP2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KP2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KP2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KP2)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PDI_HUMIN7-128
335-465		  1-
A:113-133

(-) Exons   (0, 0)

(no "Exon" information available for 2KP2)

(-) 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:133
 aligned with PDI_HUMIN | P55059 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:181
                                   184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354 
            PDI_HUMIN   175 YPFGSSSDAALAEAEGVKAPAIVLYKDFDEGKAVFSEKFEVEAIEKFAKTGATPLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEG 355
               SCOP domains d2kp2                                                a_ A: Protein disulfide isomerase, PDI                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------Thioredoxin_6-2kp2A01 A:6-112                                                                              --------------------- Pfam domains
         Sec.struct. author .....------------------------------------------------..eee....hhhhhhh....eeeeee....hhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh.......eeeee......eee.......hhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_2         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kp2 A   1 GPLGS------------------------------------------------PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEG 133
                                |    -         -         -         -         -   |    12        22        32        42        52        62        72        82        92       102       112       122       132 
                                5                                                6
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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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KP2)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (PDI_HUMIN | P55059)
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.
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:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDI_HUMIN | P55059: 2djj 2djk 2kp1 2rue 2ruf 3wt1 3wt2 5crw

(-) Related Entries Specified in the PDB File

6971
2kp1 A' DOMAIN OF PDI