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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST SCO1
 
Authors :  C. Abajian, A. C. Rosenzweig
Date :  04 Oct 05  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Metallochaperone, Cytochrome C Oxidase, Sco, Sco1, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abajian, A. C. Rosenzweig
Crystal Structure Of Yeast Sco1.
J. Biol. Inorg. Chem. V. 11 459 2006
PubMed-ID: 16570183  |  Reference-DOI: 10.1007/S00775-006-0096-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SCO1 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 96-295
    Gene: SCO1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PT2Ligand/IonPLATINUM (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PT-1Ligand/IonPLATINUM (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PT-1Ligand/IonPLATINUM (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1PT-1Ligand/IonPLATINUM (II) ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1PT-1Ligand/IonPLATINUM (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:474BINDING SITE FOR RESIDUE PT B 428
2AC2SOFTWAREHOH D:528BINDING SITE FOR RESIDUE PT D 429

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B7K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B7K)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR037C1YBR037C.1II:311451-310564888SCO1_YEAST1-2952954A:111-279 (gaps)
B:113-276
C:111-279 (gaps)
D:113-276		169
164
169
164

(-) 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:155
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:169
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
           SCO1_YEAST   111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPA 279
               SCOP domains d2b7ka_ A: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                           SCOP domains
               CATH domains 2b7kA00 A:111-279 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh..--------------.......eeee.....eeeee......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:111-279 (gaps) UniProt: 1-295 [INCOMPLETE]                                                                                                               Transcript 1
                 2b7k A 111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRV--------------LVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPA 279
                                   120       130       140       150       160       170       180       190       200       210       220|        -     | 240       250       260       270         
                                                                                                                                        221            236                                           


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:164
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    
           SCO1_YEAST   113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSY 276
               SCOP domains d2b7kb_ B: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                      SCOP domains
               CATH domains 2b7kB00 B:113-276 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh.......................eeee.....eeeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:113-276 UniProt: 1-295 [INCOMPLETE]                                                                                                                 Transcript 1
                 2b7k B 113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSY 276
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    


Chain C from PDB  Type:PROTEIN  Length:155
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:169
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
           SCO1_YEAST   111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPA 279
               SCOP domains d2b7kc_ C: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                           SCOP domains
               CATH domains 2b7kC00 C:111-279 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh..--------------.......eeee.....eeeee......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:111-279 (gaps) UniProt: 1-295 [INCOMPLETE]                                                                                                               Transcript 1
                 2b7k C 111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRV--------------LVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPA 279
                                   120       130       140       150       160       170       180       190       200       210       220|        -     | 240       250       260       270         
                                                                                                                                        221            236                                           


Chain D from PDB  Type:PROTEIN  Length:164
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:164
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    
           SCO1_YEAST   113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSY 276
               SCOP domains d2b7kd_ D: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                      SCOP domains
               CATH domains 2b7kD00 D:113-276 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh.......................eeee.....eeeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:113-276 UniProt: 1-295 [INCOMPLETE]                                                                                                                 Transcript 1
                 2b7k D 113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSY 276
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7K)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SCO1_YEAST | P23833)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008379    thioredoxin peroxidase activity    Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
    GO:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0008535    respiratory chain complex IV assembly    The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase), the terminal member of the respiratory chain of the mitochondrion and some aerobic bacteria. Cytochrome c oxidases are multi-subunit enzymes containing from 13 subunits in the mammalian mitochondrial form to 3-4 subunits in the bacterial forms.
    GO:0051775    response to redox state    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
cellular component
    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.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    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
        SCO1_YEAST | P23833: 2b7j

(-) Related Entries Specified in the PDB File

2b7j CRYSTAL STRUCTURE OF YEAST SCO1 WITH COPPER BOUND