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(-) Description

Title :  THE TRANSIENT COMPLEX OF POPLAR PLASTOCYANIN WITH TURNIP CYTOCHROME F DETERMINED WITH PARAMAGNETIC NMR
 
Authors :  C. Lange, T. Cornvik, I. Diaz-Moreno, M. Ubbink
Date :  09 Jun 04  (Deposition) - 24 May 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Electron Transfer, Photosynthesis, Nmr, Paramagnetic, Rigid Body Calculations (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lange, T. Cornvik, I. Diaz-Moreno, M. Ubbink
The Transient Complex Of Poplar Plastocyanin With Cytochrome F: Effects Of Ionic Strength And Ph
Biochim. Biophys. Acta V. 1707 179 2005
PubMed-ID: 15863096  |  Reference-DOI: 10.1016/J.BBABIO.2004.12.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASTOCYANIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETPC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PETE
    Organism Scientific: POPULUS NIGRA
    Organism Taxid: 3691
 
Molecule 2 - CYTOCHROME F
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Plasmid: PTC1
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Expression System Vector Type: PLASMID
    Gene: PETA
    Organism Common: TURNIP
    Organism Scientific: BRASSICA RAPA SUBSP. RAPA
    Organism Taxid: 51350
    Strain: SUBSP. RAPA

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2HEC1Ligand/IonHEME C

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:37 , CYS A:84 , HIS A:87 , MET A:92BINDING SITE FOR RESIDUE CU A 100
2AC2SOFTWAREGLN A:88 , GLY A:89 , TYR B:1 , PHE B:4 , VAL B:20 , CYS B:21 , CYS B:24 , HIS B:25 , GLN B:59 , LEU B:69 , ASN B:70 , VAL B:71 , GLY B:72 , ASN B:153 , GLY B:155 , ARG B:156 , GLY B:157 , ILE B:159 , TYR B:160BINDING SITE FOR RESIDUE HEC B 253

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 30)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10Val A:15 -Pro A:16
21, 2, 3, 4, 5, 6, 7, 8, 9, 10Phe A:35 -Pro A:36
31, 2, 3, 4, 5, 6, 7, 8, 9, 10Gly B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.PLAS1_POPNI147-161  1A:78-92

(-) Exons   (0, 0)

(no "Exon" information available for 1TKW)

(-) 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 A from PDB  Type:PROTEIN  Length:99
 aligned with PLAS1_POPNI | P00299 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:99
                                    79        89        99       109       119       129       139       149       159         
          PLAS1_POPNI    70 IDVLLGADDGSLAFVPSEFSISPGEKIVFKNNAGFPHNIVFDEDSIPSGVDASKISMSEEDLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN 168
               SCOP domains d1tkwa_ A: Plastocyanin                                                                             SCOP domains
               CATH domains 1tkwA00 A:1-99 Cupredoxins -  blue copper proteins                                                  CATH domains
               Pfam domains Copper-bind-1tkwA01 A:1-99                                                                          Pfam domains
         Sec.struct. author .eeee........ee..eeee....eeeeee........ee.........hhhhh.............eeeee....eeeeee.........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1tkw A   1 IDVLLGADDGSLAFVPSEFSISPGEKIVFKNNAGFPHNIVFDEDSIPSGVDASKISMSEEDLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN  99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with CYF_BRARR | P36438 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
            CYF_BRARR    36 YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1tkwB01 B:1-170,B:230-250  [code=2.60.40.830, no name defined]                                                                                                            1tkwB02 B:171-229  [code=2.40.50.100, no name defined]     1tkwB01               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.........hhhhhh.......eee...ee....eeeeeee........ee.....ee..eeeeeee.....ee.hhhhhhhhhhhhh.....eeee..eeeeeeeeeeehhhhheeeeeee..hhhhh......eeeeeeeeee......................eeeeeeee.....eeeeeee....eeeeeee............ee.............eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tkw B   1 YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (3, 3)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (14, 22)

NMR Structure(hide GO term definitions)
Chain A   (PLAS1_POPNI | P00299)
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.

Chain B   (CYF_BRARR | P36438)
molecular function
    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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
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: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:0031361    integral component of thylakoid membrane    The component of the thylakoid membrane consisting of the gene products 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: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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  PLAS1_POPNI | P00299
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYF_BRARR | P36438: 1ctm 1hcz 1jx8 2pcf
        PLAS1_POPNI | P00299: 1jxg 1plc 1pnc 1pnd 2pcy 3pcy 4dp7 4dp8 4dp9 4dpa 4dpb 4dpc 4pcy 5pcy 6pcy

(-) Related Entries Specified in the PDB File

1hcz CYTOCHROME F FROM BRASSICA RAPA (TURNIP)
2pcf COMPLEX OF SPINACH PLASTOCYANIN AND TURNIP CYTOCHROME F DETERMINED WITH PARAMAGNETIC NMR
5pcy POPULUS SP. PLASTOCYANIN (CUI, PH 7)