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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C30S/C133S MUTANT OF ERV1 FROM SACCHAROMYCES CEREVISIAE
 
Authors :  P. C. Guo, J. D. Ma, Y. L. Jiang, S. J. Wang, T. T. Hu, Y. X. Chen, C. Z. Zhou
Date :  04 Mar 12  (Deposition) - 29 Aug 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Flavin-Linked Sulfhydryl Oxidase, Mia40, Oxidation, Mitochondrial Intermembrane Space, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. C. Guo, J. D. Ma, Y. L. Jiang, S. J. Wang, Z. Z. Bao, X. J. Yu, Y. Chen, C. Z. Zhou
Structure Of Yeast Sulfhydryl Oxidase Erv1 Reveals Electron Transfer Of The Disulfide Relay System In The Mitochondrial Intermembrane Space
J. Biol. Chem. V. 287 34961 2012
PubMed-ID: 22910915  |  Reference-DOI: 10.1074/JBC.M112.394759

(-) Compounds

Molecule 1 - MITOCHONDRIAL FAD-LINKED SULFHYDRYL OXIDASE ERV1
    ChainsA, B, C
    EC Number1.8.3.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneYGR029W
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainS288C
    Synonym14 KDA REGULATORY PROTEIN, ESSENTIAL FOR RESPIRATION AND VEGETATIVE GROWTH PROTEIN 1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)AB 
Biological Unit 2 (2x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1FAD3Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:88 , GLY A:91 , ARG A:92 , SER A:94 , TRP A:95 , HIS A:99 , TYR A:128 , SER A:133 , CYS A:159 , HIS A:162 , ASN A:163 , VAL A:165 , ASN A:166 , LYS A:168 , LEU A:169 , LYS A:171 , PHE A:174 , ARG A:182 , TRP A:183 , TYR B:79 , GLU C:88BINDING SITE FOR RESIDUE FAD A 201
2AC2SOFTWAREVAL B:87 , GLY B:91 , ARG B:92 , TRP B:95 , HIS B:99 , TYR B:128 , TRP B:132 , SER B:133 , CYS B:159 , HIS B:162 , ASN B:163 , VAL B:165 , ASN B:166 , LYS B:168 , LEU B:169 , LYS B:171 , PHE B:174 , ARG B:182 , TRP B:183BINDING SITE FOR RESIDUE FAD B 201
3AC3SOFTWAREGLU A:88 , TYR C:79 , GLU C:88 , GLY C:91 , ARG C:92 , SER C:94 , TRP C:95 , HIS C:99 , TYR C:128 , TRP C:132 , SER C:133 , PHE C:137 , CYS C:159 , HIS C:162 , ASN C:163 , VAL C:165 , ASN C:166 , LYS C:168 , LEU C:169 , LYS C:171 , PHE C:174 , ARG C:182 , TRP C:183BINDING SITE FOR RESIDUE FAD C 201

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:33 -B:130
2A:159 -A:176
3B:159 -B:176
4C:159 -C:176

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:74 -Gly B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E0I)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.ERV1_YEAST83-183
 
 
  3A:83-183
B:83-183
C:83-183
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.ERV1_YEAST83-183
 
 
  2A:83-183
B:83-183
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.ERV1_YEAST83-183
 
 
  2-
-
C:83-183

(-) Exons   (0, 0)

(no "Exon" information available for 4E0I)

(-) 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:152
 aligned with ERV1_YEAST | P27882 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:175
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
           ERV1_YEAST    14 EGLSGRKIIYDEDGKPCRSCNTLLDFQYVTGKISNGLKNLSSNGKLAGTGALTGEASELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee............hhhhhhhhhh...-----------------------...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ERV_ALR  PDB: A:83-183 UniProt: 83-183                                                               ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e0i A  14 EGLSGRKIIYDEDGKPSRSCNTLLDFQYVTGKIS-----------------------ELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWSAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
                                    23        33        43   |     -         -       |73        83        93       103       113       123       133       143       153       163       173       183     
                                                            47                      71                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with ERV1_YEAST | P27882 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:119
                                    79        89        99       109       119       129       139       149       159       169       179         
           ERV1_YEAST    70 SELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
               SCOP domains d4e0ib_ B: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------ERV_ALR  PDB: B:83-183 UniProt: 83-183                                                               ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4e0i B  70 SELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWSAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
                                    79        89        99       109       119       129       139       149       159       169       179         

Chain C from PDB  Type:PROTEIN  Length:118
 aligned with ERV1_YEAST | P27882 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:118
                                    80        90       100       110       120       130       140       150       160       170       180        
           ERV1_YEAST    71 ELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
               SCOP domains d4e0ic_ C: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------ERV_ALR  PDB: C:83-183 UniProt: 83-183                                                               ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4e0i C  71 ELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWSAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
                                    80        90       100       110       120       130       140       150       160       170       180        

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E0I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E0I)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ERV1_YEAST | P27882)
molecular function
    GO:0016971    flavin-linked sulfhydryl oxidase activity    Catalysis of the formation of disulfide bridges.
    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: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: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:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0034599    cellular response to oxidative 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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0045041    protein import into mitochondrial intermembrane space    The import of proteins into the space between the inner and outer mitochondrial membranes.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
cellular component
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ERV1_YEAST | P278823w4y 4e0h

(-) Related Entries Specified in the PDB File

4e0h