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(-) Description

Title :  STRUCTURE OF ERO1P, SOURCE OF DISULFIDE BONDS FOR OXIDATIVE PROTEIN FOLDING IN THE CELL
 
Authors :  E. Gross, D. B. Kastner, C. A. Kaiser, D. Fass
Date :  04 Dec 03  (Deposition) - 08 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavoenzyme, Disulfide Bonds, Cxxcxxc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Gross, D. B. Kastner, C. A. Kaiser, D. Fass
Structure Of Ero1P, Source Of Disulfide Bonds For Oxidative Protein Folding In The Cell.
Cell(Cambridge, Mass. ) V. 117 601 2004
PubMed-ID: 15163408  |  Reference-DOI: 10.1016/S0092-8674(04)00418-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 65.0 KDA PROTEIN IN COX14-COS3 INTERGENIC REGION PRECURSOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YML130C, YM4987.05C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NEN1Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:237 , GLU A:241 , GLU A:408 , HOH A:829BINDING SITE FOR RESIDUE CD A 813
2AC2SOFTWAREHIS A:386 , LYS A:390BINDING SITE FOR RESIDUE CD A 814
3AC3SOFTWAREGLN A:205 , CYS A:208 , TYR A:420BINDING SITE FOR RESIDUE NEN A 501
4AC4SOFTWAREASP A:108 , GLU A:186 , ARG A:187 , PHE A:188 , THR A:189 , GLY A:190 , TYR A:191 , ALA A:196 , ILE A:199 , TRP A:200 , TYR A:204 , TYR A:224 , SER A:228 , HIS A:231 , ALA A:232 , ILE A:234 , LEU A:238 , ARG A:260 , ARG A:267 , MET A:347 , CYS A:355 , HOH A:820 , HOH A:871BINDING SITE FOR RESIDUE FAD A 634

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:90 -A:349
2A:100 -A:105
3A:143 -A:166
4A:150 -A:295
5A:352 -A:355

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RQ1)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YML130C1YML130C.1XIII:13175-114841692ERO1_YEAST1-5635631A:54-424 (gaps)371

(-) Sequences/Alignments

Asymmetric/Biological 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:356
 aligned with ERO1_YEAST | Q03103 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:371
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
           ERO1_YEAST    54 VTFNELNAINENIRDDLSALLKSDFFKYFRLDLYKQCSFWDANDGLCLNRACSVDVVEDWDTLPEYWQPEILGSFNNDTMKEADDSDDECKFLDQLCQTSKKPVDIEDTINYCDVNDFNGKNAVLIDLTANPERFTGYGGKQAGQIWSTIYQDNCFTIGETGESLAKDAFYRLVSGFHASIGTHLSKEYLNTKTGKWEPNLDLFMARIGNFPDRVTNMYFNYAVVAKALWKIQPYLPEFSFCDLVNKEIKNKMDNVISQLDTKIFNEDLVFANDLSLTLKDEFRSRFKNVTKIMDCVQCDRCRLWGKIQTTGYATALKILFEINDADEFTKQHIVGKLTKYELIALLQTFGRLSESIESVNMFEKMYGKRL 424
               SCOP domains d1rq1a_ A: Endoplasmic oxidoreductin 1,      Ero1p                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------ERO1-1rq1A01 A:64-414                                                                                                                                                                                                                                                                                                                                          ---------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhheeeee........-----...hhhhh.....hhhhhhhhhhhhhhh......eee.........hhhhh......---------...........eeeee...........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhee......ee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh-hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:54-424 (gaps) UniProt: 1-563 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                          Transcript 1
                 1rq1 A  54 GSFNELNAINENIRDDLSALLKSDFFKYFRLDLYKQCSFW-----LCLNRACSVDVVEDWDTLPEYWQPEILGSFNNDTMKEADDSDDECKFLDQLCQTSKK---------YCDVNDFNGKNAVLIDLTANPERFTGYGGKQAGQIWSTIYQDNCFTIGETGESLAKDAFYRLVSGFHASIGTHLSKEYLNTKTGKWEPNLDLFMARIGNFPDRVTNMYFNYAVVAKALWKIQPYLPEFSFCDLVNKEIKNKMDNVISQLDTKIFNEDLVFANDLSLTLKDEFRSRF-NVTKIMDCVQCDRCRLWGKIQTTGYATALKILFEINDADEFTKQHIVGKLTKYELIALLQTFGRLSESIESVNMFEKMYGKRL 424
                                    63        73        83        93     | 103       113       123       133       143       153 |       - |     173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333      |343       353       363       373       383       393       403       413       423 
                                                                  93    99                                                     155       165                                                                                                                                                                            340 |                                                                                  
                                                                                                                                                                                                                                                                                                                          342
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RQ1)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: ERO1] (4)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERO1_YEAST | Q03103)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
    GO:0016972    thiol oxidase activity    Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O.
biological process
    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: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).
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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1rq1
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERO1_YEAST | Q03103: 1rp4 3m31 3nvj

(-) Related Entries Specified in the PDB File

1rp4 STRUCTURE FROM A DIFFERENT CRYSTAL FORM OF ERO1P