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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE REDUCED SPINACH PLASTOCYANIN
 
Authors :  F. Musiani, A. Dikiy, A. Y. Semenov, S. Ciurli
Date :  19 Jan 05  (Deposition) - 05 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  B
Keywords :  Plastocyanin, Copper(+)-Containing, Electron-Transfer, Spinach, Photosynthesis, Blue-Copper Protein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Musiani, A. Dikiy, A. Y. Semenov, S. Ciurli
Structure Of The Intermolecular Complex Between Plastocyanin And Cytochrome F From Spinach.
J. Biol. Chem. V. 280 18833 2005
PubMed-ID: 15691836  |  Reference-DOI: 10.1074/JBC.M412760200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASTOCYANIN, CHLOROPLAST
    Chains: B
    Fragment: REDUCED SPINACH PLASTOCYANIN (RESIDUES 70-168)
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:37 , CYS B:84 , HIS B:87BINDING SITE FOR RESIDUE CU1 B 100

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

NMR Structure
No.Residues
1Leu B:15 -Pro B:16
2Phe B:35 -Pro B:36

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.PLAS_SPIOL147-161  1B:78-92

(-) Exons   (0, 0)

(no "Exon" information available for 1YLB)

(-) Sequences/Alignments

NMR Structure
   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 B from PDB  Type:PROTEIN  Length:99
 aligned with PLAS_SPIOL | P00289 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:99
                                    79        89        99       109       119       129       139       149       159         
           PLAS_SPIOL    70 VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN 168
               SCOP domains d1ylbb_ B: automated matches                                                                        SCOP domains
               CATH domains 1ylbB00 B:1-99 Cupredoxins -  blue copper proteins                                                  CATH domains
               Pfam domains Copper-bind-1ylbB01 B:1-99                                                                          Pfam domains
         Sec.struct. author .eeee........ee..........eeeeee........ee.........hhhhh.............eeeee.....eeeee.........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1ylb B   1 VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN  99
                                    10        20        30        40        50        60        70        80        90
   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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain B   (PLAS_SPIOL | P00289)
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_SPIOL | P00289: 1ag6 1oow 1tef 1teg 2pcf

(-) Related Entries Specified in the PDB File

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