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(-) Description

Title :  OXIDIZED AND REDUCED STRUCTURES OF A MUTANT PLASTOCYANIN OF FERN
 
Authors :  R. Hulsker, E. A. J. Thomassen, M. Ubbink
Date :  15 Aug 05  (Deposition) - 20 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Plastocyanin, Fern, Chloroplast, Electron Transport, Membrane, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hulsker, A. Mery, E. A. J. Thomassen, A. Ranieri, M. Sola, M. P. Verbeet, T. Kohzuma, M. Ubbink
Protonation Of A Histidine Copper Ligand In Fern Plastocyanin.
J. Am. Chem. Soc. V. 129 4423 2007
PubMed-ID: 17367139  |  Reference-DOI: 10.1021/JA0690464
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASTOCYANIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETG36P
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28C
    Mutation: YES
    Organism Common: FERN
    Organism Scientific: DRYOPTERIS CRASSIRHIZOMA
    Organism Taxid: 97234
    Other Details: REDUCED FORM THE REDUCED FORM WAS OBTAINED BY REDUCING THE OXIDIZED CRYSTAL FOR 10 MINUTES IN CRYSTALLISATION BUFFER INCLUDING 0.01M SODIUM ASCORBATE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:37 , CYS A:87 , HIS A:90 , MET A:95BINDING SITE FOR RESIDUE CU1 A 103

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:15 -Pro A:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.PLAS_DRYCA81-95  1A:81-95

(-) Exons   (0, 0)

(no "Exon" information available for 2BZC)

(-) 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:102
 aligned with PLAS_DRYCA | Q7SIB8 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:102
                                    10        20        30        40        50        60        70        80        90       100  
           PLAS_DRYCA     1 AKVEVGDEVGNFKFYPDSITVSAGEAVEFTLVGETGHNIVFDIPAGAPGTVASELKAASMDENDLLSEDEPSFKAKVSTPGTYTFYCTPHKSANMKGTLTVK 102
               SCOP domains d2bzca_ A: Plastocyanin                                                                                SCOP domains
               CATH domains 2bzcA00 A:1-102 Cupredoxins -  blue copper proteins                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee........ee..eeee....eeeeee........ee......hhhhhhhhhhh.............eeeee....eeeeee.........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2bzc A   1 AKVEVGDEVGNFKFYPDSITVSAGEAVEFTLVGETPHNIVFDIPAGAPGTVASELKAASMDENDLLSEDEPSFKAKVSTPGTYTFYCTPHKSANMKGTLTVK 102
                                    10        20        30        40        50        60        70        80        90       100
   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 beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLAS_DRYCA | Q7SIB8)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLAS_DRYCA | Q7SIB8: 1kdi 1kdj 2bz7

(-) Related Entries Specified in the PDB File

1kdi REDUCED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA
1kdj OXIDIZED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA
2bz7 OXIDIZED AND REDUCED STRUCTURES OF A MUTANT PLASTOCYANIN OF FERN