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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRUNCATED FORM OF YEAST COPPER THIONEIN
 
Authors :  V. Calderone, B. Dolderer, H. J. Hartmann, H. Echner, C. Luchinat, C. Del Bianco, S. Mangani, U. Weser
Date :  20 Nov 03  (Deposition) - 07 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  V
Keywords :  Yeast Cu(I) Metallothionein, Cu(I) Metallothionein Fragments, Cu(I)-Thiolate, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Calderone, B. Dolderer, H. J. Hartmann, H. Echner, C. Luchinat, C. Del Bianco, S. Mangani, U. Weser
The Crystal Structure Of Yeast Copper Thionein: The Solution Of A Long Lasting Enigma.
Proc. Natl. Acad. Sci. Usa V. 102 51 2005
PubMed-ID: 15613489  |  Reference-DOI: 10.1073/PNAS.0408254101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLOTHIONEIN
    Chains: V
    Engineered: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
    Synonym: CU-MT, COPPER CHELATIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : V

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1CU18Ligand/IonCOPPER (I) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS V:3 , CYS V:5 , CYS V:20 , CU1 V:38 , CU1 V:39 , CU1 V:42BINDING SITE FOR RESIDUE CU1 V 37
2AC2SOFTWARECYS V:3 , CYS V:10 , CYS V:16 , GLN V:17 , CU1 V:37 , CU1 V:43BINDING SITE FOR RESIDUE CU1 V 38
3AC3SOFTWARECYS V:5 , CYS V:10 , CYS V:20 , CYS V:22 , CU1 V:37 , CU1 V:40 , CU1 V:41 , CU1 V:42 , CU1 V:43 , CU1 V:44BINDING SITE FOR RESIDUE CU1 V 39
4AC4SOFTWARECYS V:7 , CYS V:10 , CYS V:32 , CU1 V:39 , CU1 V:41 , CU1 V:44BINDING SITE FOR RESIDUE CU1 V 40
5AC5SOFTWARECYS V:22 , CYS V:26 , CYS V:32 , PRO V:33 , CU1 V:39 , CU1 V:40 , CU1 V:44BINDING SITE FOR RESIDUE CU1 V 41
6AC6SOFTWARECYS V:10 , CYS V:20 , CYS V:22 , CYS V:34 , CU1 V:37 , CU1 V:39 , CU1 V:43BINDING SITE FOR RESIDUE CU1 V 42
7AC7SOFTWARECYS V:10 , CYS V:16 , CYS V:34 , CU1 V:38 , CU1 V:39 , CU1 V:42BINDING SITE FOR RESIDUE CU1 V 43
8AC8SOFTWARECYS V:5 , CYS V:7 , CYS V:26 , CYS V:32 , CU1 V:39 , CU1 V:40 , CU1 V:41BINDING SITE FOR RESIDUE CU1 V 44

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RJU)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YHR055C1YHR055C.1VIII:214720-214535186MTCU2_YEAST1-61611V:1-3636

(-) 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 V from PDB  Type:PROTEIN  Length:36
 aligned with MTCU1_YEAST | P0CX80 from UniProtKB/Swiss-Prot  Length:61

    Alignment length:36
                                    22        32        42      
           MTCU1_YEAST   13 HECQCQCGSCKNNEQCQKSCSCPTGCNSDDKCPCGN 48
               SCOP domains d1rjuv_ V: Metallothionein           SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ............hhhhh..........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                  1rju V  1 HECQCQCGSCKNNEQCQKSCSCPTGCNSDDKCPCGN 36
                                    10        20        30      


Chain V from PDB  Type:PROTEIN  Length:36
 aligned with MTCU2_YEAST | P0CX81 from UniProtKB/Swiss-Prot  Length:61

    Alignment length:36
                                    22        32        42      
           MTCU2_YEAST   13 HECQCQCGSCKNNEQCQKSCSCPTGCNSDDKCPCGN 48
               SCOP domains d1rjuv_ V: Metallothionein           SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ............hhhhh..........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: V:1-36 UniProt: 1-61  Transcript 1
                  1rju V  1 HECQCQCGSCKNNEQCQKSCSCPTGCNSDDKCPCGN 36
                                    10        20        30
   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: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RJU)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain V   (MTCU1_YEAST | P0CX80)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0046870    cadmium ion binding    Interacting selectively and non-covalently with cadmium (Cd) ions.
    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:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
    GO:0071585    detoxification of cadmium ion    Any process that reduces or removes the toxicity of cadmium ion. These may include transport of cadmium away from sensitive areas and to compartments or complexes whose purpose is sequestration of cadmium ion.
    GO:0010273    detoxification of copper ion    Any process that reduces or removes the toxicity of copper ion. These include transport of copper away from sensitive areas and to compartments or complexes whose purpose is sequestration of copper ion.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0046688    response to copper ion    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 copper ion stimulus.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain V   (MTCU2_YEAST | P0CX81)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0046870    cadmium ion binding    Interacting selectively and non-covalently with cadmium (Cd) ions.
    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:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
    GO:0071585    detoxification of cadmium ion    Any process that reduces or removes the toxicity of cadmium ion. These may include transport of cadmium away from sensitive areas and to compartments or complexes whose purpose is sequestration of cadmium ion.
    GO:0010273    detoxification of copper ion    Any process that reduces or removes the toxicity of copper ion. These include transport of copper away from sensitive areas and to compartments or complexes whose purpose is sequestration of copper ion.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0046688    response to copper ion    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 copper ion stimulus.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTCU1_YEAST | P0CX80: 1aoo 1aqq 1aqr 1aqs 1fmy
        MTCU2_YEAST | P0CX81: 1aoo 1aqq 1aqr 1aqs 1fmy

(-) Related Entries Specified in the PDB File

1fmy NMR STRUCTURE OF THE PROTEIN PART OF CU7 METALLOTHIONEIN