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(-) Description

Title :  CRYSTAL STRUCTURE OF ERV2P
 
Authors :  E. Gross, C. S. Sevier, A. Vala, C. A. Kaiser, D. Fass
Date :  13 Aug 01  (Deposition) - 28 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fad, Sulfhydryl Oxidase, Helical Bundle, Cxxc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Gross, C. S. Sevier, A. Vala, C. A. Kaiser, D. Fass
A New Fad-Binding Fold And Intersubunit Disulfide Shuttle In The Thiol Oxidase Erv2P.
Nat. Struct. Biol. V. 9 61 2002
PubMed-ID: 11740506  |  Reference-DOI: 10.1038/NSB740
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERV2 PROTEIN, MITOCHONDRIAL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAED4
    Expression System Strain: BL21 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTEASE-RESISTANT DOMAIN
    Gene: ERV2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ERV2P SULFHYDRYL OXIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/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  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:11 , GLY B:15 , ARG B:16 , SER B:18 , TRP B:19 , HIS B:23 , TYR B:52 , CYS B:57 , HIS B:60 , PHE B:61 , CYS B:83 , HIS B:86 , ASN B:87 , VAL B:89 , ASN B:90 , LEU B:93 , LYS B:95 , TYR B:98 , ILE B:103 , TYR B:107 , HOH B:347 , HOH B:348 , HOH B:351 , HOH B:363 , HOH B:375 , HOH B:392 , LYS D:9 , ARG D:16BINDING SITE FOR RESIDUE FAD B 334
2AC2SOFTWARELYS A:11 , GLY A:15 , ARG A:16 , SER A:18 , TRP A:19 , HIS A:23 , TYR A:48 , TYR A:52 , CYS A:57 , PHE A:61 , CYS A:83 , HIS A:86 , ASN A:87 , VAL A:89 , ASN A:90 , LEU A:93 , LYS A:95 , TYR A:98 , ILE A:103 , TYR A:107 , HOH A:352 , HOH A:356 , HOH A:375 , HOH A:384 , HOH A:385 , HOH A:386 , HOH A:387BINDING SITE FOR RESIDUE FAD A 335
3AC3SOFTWARELYS D:11 , GLY D:15 , ARG D:16 , SER D:18 , TRP D:19 , HIS D:23 , TYR D:48 , TYR D:52 , CYS D:57 , PHE D:61 , CYS D:83 , HIS D:86 , ASN D:87 , VAL D:89 , ASN D:90 , TYR D:92 , LEU D:93 , LYS D:95 , TYR D:98 , TYR D:107 , HOH D:347 , HOH D:354 , HOH D:371 , HOH D:372 , HOH D:373 , HOH D:392BINDING SITE FOR RESIDUE FAD D 336
4AC4SOFTWAREHOH A:386 , LYS C:11 , LYS C:12 , GLY C:15 , ARG C:16 , SER C:18 , TRP C:19 , HIS C:23 , TYR C:48 , TYR C:52 , GLU C:56 , CYS C:57 , HIS C:60 , PHE C:61 , CYS C:83 , HIS C:86 , ASN C:87 , VAL C:89 , ASN C:90 , TYR C:92 , LEU C:93 , LYS C:95 , TYR C:98 , ILE C:103 , TYR C:107 , HOH C:365 , HOH C:366 , HOH C:370 , HOH C:371 , HOH C:403 , HOH C:404BINDING SITE FOR RESIDUE FAD C 337

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:54 -A:57
2A:83 -A:100
3A:109 -A:111
4B:54 -B:57
5B:83 -B:100
6B:109 -B:111
7C:54 -C:57
8C:83 -C:100
9C:109 -C:111
10D:54 -D:57
11D:83 -D:100
12D:109 -D:111

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR037C1YPR037C.1XVI:647035-646445591ERV2_YEAST1-1961964A:7-112
B:7-112
C:7-111
D:9-111		106
106
105
103

(-) 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:106
 aligned with ERV2_YEAST | Q12284 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:106
                                    83        93       103       113       123       133       143       153       163       173      
           ERV2_YEAST    74 DDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGCS 179
               SCOP domains d1jraa_ A: Thiol oxidase Erv2p                                                                             SCOP domains
               CATH domains 1jraA00 A:7-112  [code=1.20.120.310, no name defined]                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:7-112 UniProt: 1-196 [INCOMPLETE]                                                         Transcript 1
                 1jra A   7 DDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGCS 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with ERV2_YEAST | Q12284 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:106
                                    83        93       103       113       123       133       143       153       163       173      
           ERV2_YEAST    74 DDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGCS 179
               SCOP domains d1jrab_ B: Thiol oxidase Erv2p                                                                             SCOP domains
               CATH domains 1jraB00 B:7-112  [code=1.20.120.310, no name defined]                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:7-112 UniProt: 1-196 [INCOMPLETE]                                                         Transcript 1
                 1jra B   7 DDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGCS 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain C from PDB  Type:PROTEIN  Length:105
 aligned with ERV2_YEAST | Q12284 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:105
                                    83        93       103       113       123       133       143       153       163       173     
           ERV2_YEAST    74 DDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGC 178
               SCOP domains d1jrac_ C: Thiol oxidase Erv2p                                                                            SCOP domains
               CATH domains 1jraC00 C:7-111  [code=1.20.120.310, no name defined]                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:7-111 UniProt: 1-196 [INCOMPLETE]                                                        Transcript 1
                 1jra C   7 DDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGC 111
                                    16        26        36        46        56        66        76        86        96       106     


Chain D from PDB  Type:PROTEIN  Length:103
 aligned with ERV2_YEAST | Q12284 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:103
                                    85        95       105       115       125       135       145       155       165       175   
           ERV2_YEAST    76 KVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGC 178
               SCOP domains d1jrad_ D: Thiol oxidase Erv2p                                                                          SCOP domains
               CATH domains 1jraD00 D:9-111  [code=1.20.120.310, no name defined]                                                   CATH domains
           Pfam domains (1) -------Evr1_Alr-1jraD01 D:16-109                                                                     -- Pfam domains (1)
           Pfam domains (2) -------Evr1_Alr-1jraD02 D:16-109                                                                     -- Pfam domains (2)
           Pfam domains (3) -------Evr1_Alr-1jraD03 D:16-109                                                                     -- Pfam domains (3)
           Pfam domains (4) -------Evr1_Alr-1jraD04 D:16-109                                                                     -- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:9-111 UniProt: 1-196 [INCOMPLETE]                                                      Transcript 1
                 1jra D   9 KVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGC 111
                                    18        28        38        48        58        68        78        88        98       108
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Evr1_Alr] (7)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ERV2_YEAST | Q12284)
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: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.
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:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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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  1jra
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  ERV2_YEAST | Q12284
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERV2_YEAST | Q12284: 1jr8

(-) Related Entries Specified in the PDB File

1jr8 1JR8 IS A DIFFERENT CRYSTAL FORM OF THE SAME PROTEIN