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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YEAST DITHIOL/DISULFIDE OXIDOREDUCTASE MPD1P
 
Authors :  E. Vitu, H. M. Greenblatt, D. Fass
Date :  02 Sep 08  (Deposition) - 04 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Thioredoxin-Like Domain, Cxxc, Isomerase, Endoplasmic Reticulum, Glycoprotein, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Vitu, E. Gross, H. M. Greenblatt, C. S. Sevier, C. A. Kaiser, D. Fass
Yeast Mpd1P Reveals The Structural Diversity Of The Protein Disulfide Isomerase Family
J. Mol. Biol. V. 384 631 2008
PubMed-ID: 18845159  |  Reference-DOI: 10.1016/J.JMB.2008.09.052
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE MPD1
    Chains: A, B
    EC Number: 5.3.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-310
    Gene: MPD1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:48 , GLY A:78 , LYS A:298 , HOH A:2811BINDING SITE FOR RESIDUE ACT A 1101
02AC2SOFTWAREGLY B:78 , LYS B:298 , HOH B:2794 , HOH B:2822BINDING SITE FOR RESIDUE ACT B 1102
03AC3SOFTWAREASP B:77 , GLY B:78 , LYS B:298BINDING SITE FOR RESIDUE ACT B 1103
04AC4SOFTWAREASP A:40 , HIS A:44 , LYS A:98BINDING SITE FOR RESIDUE ACT A 1105
05AC5SOFTWAREGLN A:184 , SER A:188 , ASP B:243 , LYS B:244BINDING SITE FOR RESIDUE ACT A 1106
06AC6SOFTWAREASN A:45 , THR A:46 , ASN A:47BINDING SITE FOR RESIDUE ACT A 1108
07AC7SOFTWAREASP A:40 , LEU A:95 , HOH A:2766 , HOH A:2817BINDING SITE FOR RESIDUE ACT A 1109
08AC8SOFTWAREARG A:111 , PRO A:113 , ALA A:132 , ARG A:154BINDING SITE FOR RESIDUE EDO A 2762
09AC9SOFTWAREALA A:42 , THR A:46 , TYR A:48 , GLN A:81 , GLU A:284 , ARG A:290 , ILE A:294 , HOH A:2808BINDING SITE FOR RESIDUE EDO A 2763
10BC1SOFTWAREALA B:42 , THR B:46 , TYR B:48 , GLN B:81 , GLU B:284 , ARG B:290 , ILE B:294 , HOH B:2820BINDING SITE FOR RESIDUE EDO B 2764
11BC2SOFTWARELYS B:114 , ARG B:154 , SER B:155 , TYR B:156BINDING SITE FOR RESIDUE EDO B 2765

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:59 -A:62
2A:87 -A:96
3B:59 -B:62
4B:87 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:104 -Pro A:105
2Phe B:104 -Pro B:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ED3)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.MPD1_YEAST51-69
 		  2A:51-69
B:51-69
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.MPD1_YEAST51-69
 		  1A:51-69
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.MPD1_YEAST51-69
 		  1-
B:51-69

(-) Exons   (0, 0)

(no "Exon" information available for 3ED3)

(-) Sequences/Alignments

Asymmetric Unit
   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:267
 aligned with MPD1_YEAST | Q12404 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:280
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
           MPD1_YEAST    22 QNFYDSDPHISELTPKSFDKAIHNTNYTSLVEFYAPWCGHCKKLSSTFRKAAKRLDGVVQVAAVNCDLNKNKALCAKYDVNGFPTLMVFRPPKIDLSKPIDNAKKSFSAHANEVYSGARTLAPIVDFSLSRIRSYVKKFVRIDTLGSLLRKSPKLSVVLFSKQDKISPVYKSIALDWLGKFDFYSISNKKLKQLTDMNPTYEKTPEIFKYLQKVIPEQRQSDKSKLVVFDADKDKFWEYEGNSINKNDISKFLRDTFSITPNEGPFSRRSEYIAYLKTGK 301
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.hhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh......eeeeee....-------------...eeee.....hhhhhhhhhhh.....eee..hhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeeeee.hhh............hhhhhhhhhhhhhhhh.....eeeeee....eeee......hhhhhhhhhhhhhh........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed3 A  22 HNFYDSDPHISELTPKSFDKAIHNTNYTSLVEFYAPWCGHCKKLSSTFRKAAKRLDGVVQVAAVNCDLNKNKALCAKYDVNGFPTLMVFRPPKI-------------SAHANEVYSGARTLAPIVDFSLSRIRSYVKKFVRIDTLGSLLRKSPKLSVVLFSKQDKISPVYKSIALDWLGKFDFYSISNKKLKQLTDMNPTYEKTPEIFKYLQKVIPEQRQSDKSKLVVFDADKDKFWEYEGNSINKNDISKFLRDTFSITPNEGPFSRRSEYIAYLKTGK 301
                                    31        41        51        61        71        81        91       101       111   |     -       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
                                                                                                                       115           129                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with MPD1_YEAST | Q12404 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:279
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291         
           MPD1_YEAST    22 QNFYDSDPHISELTPKSFDKAIHNTNYTSLVEFYAPWCGHCKKLSSTFRKAAKRLDGVVQVAAVNCDLNKNKALCAKYDVNGFPTLMVFRPPKIDLSKPIDNAKKSFSAHANEVYSGARTLAPIVDFSLSRIRSYVKKFVRIDTLGSLLRKSPKLSVVLFSKQDKISPVYKSIALDWLGKFDFYSISNKKLKQLTDMNPTYEKTPEIFKYLQKVIPEQRQSDKSKLVVFDADKDKFWEYEGNSINKNDISKFLRDTFSITPNEGPFSRRSEYIAYLKTG 300
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....hhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh......eeeeee....-------------...eeee.....hhhhhhhhhhh.....eee..hhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhh...eeeeeee.hhh......hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee....eeee......hhhhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------THIOREDOXIN_1      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed3 B  22 HNFYDSDPHISELTPKSFDKAIHNTNYTSLVEFYAPWCGHCKKLSSTFRKAAKRLDGVVQVAAVNCDLNKNKALCAKYDVNGFPTLMVFRPPKI-------------SAHANEVYSGARTLAPIVDFSLSRIRSYVKKFVRIDTLGSLLRKSPKLSVVLFSKQDKISPVYKSIALDWLGKFDFYSISNKKLKQLTDMNPTYEKTPEIFKYLQKVIPEQRQSDKSKLVVFDADKDKFWEYEGNSINKNDISKFLRDTFSITPNEGPFSRRSEYIAYLKTG 300
                                    31        41        51        61        71        81        91       101       111   |     -       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291         
                                                                                                                       115           129
   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 3ED3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ED3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ED3)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MPD1_YEAST | Q12404)
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: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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    GO:0019153    protein-disulfide reductase (glutathione) activity    Catalysis of the reaction: 2 glutathione + protein-disulfide = oxidized glutathione + protein-dithiol.
biological process
    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: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: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

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(-) Related Entries Specified in the PDB File

2b5e CRYSAL STRUCTURE OF THE YEAST DITHIOL/DISULFIDE OXIDOREDUCTASE PDI1P