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(-) Description

Title :  STRUCTURE OF OXIDIZED ARABIDOPSIS THALIANA CYTOCHROME 6A
 
Authors :  M. J. Marcaida, B. G. Schlarb-Ridley, J. A. R. Worrall, J. Wastl, T. J. Evans, D. S. Bendall, B. F. Luisi, C. J. Howe
Date :  01 Feb 06  (Deposition) - 05 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym./Biol. Unit :  A
Keywords :  Chloroplast, Electron Transport, Heme, Iron, Thylakoid, Photosynthesis, Metal-Binding, Electron Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Marcaida, B. G. Schlarb-Ridley, J. A. R. Worrall, J. Wastl, T. J. Evans, D. S. Bendall, B. F. Luisi, C. J. Howe
Structure Of Cytochrome C(6A), A Novel Dithio- Cytochrome Of Arabidopsis Thaliana, And Its Reactivity With Plastocyanin: Implications For Function.
J. Mol. Biol. V. 360 968 2006
PubMed-ID: 16815443  |  Reference-DOI: 10.1016/J.JMB.2006.05.065

(-) Compounds

Molecule 1 - CYTOCHROME C6
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBATC6A
    Expression System Strain: GM119
    Expression System Taxid: 562
    Expression System Vector: PBLUESCRIPTIISK(+)
    Fragment: CYTOCHROME C6, RESIDUES 71-175
    Mutation: YES
    Organism Common: MOUSE EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: HEME GROUP AND DISULPHIDE BOND BETWEEN C67 AND C73
    Synonym: ARABIDOPSIS CYTOCHROME C6A

 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
1HEC1Ligand/IonHEME C

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:15 , CYS A:16 , CYS A:19 , HIS A:20 , ASN A:25 , ILE A:27 , GLN A:28 , ALA A:31 , THR A:32 , LEU A:33 , ASP A:37 , ASN A:41 , VAL A:43 , VAL A:52 , THR A:53 , LYS A:57 , MET A:60 , HOH A:2045 , HOH A:2064 , HOH A:2131BINDING SITE FOR RESIDUE HEC A1102

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:67 -A:73

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:68 -Pro A:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CE0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_ARATH73-165  1A:3-95

(-) Exons   (0, 0)

(no "Exon" information available for 2CE0)

(-) 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:99
 aligned with CYC6_ARATH | Q93VA3 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:99
                                    82        92       102       112       122       132       142       152       162         
           CYC6_ARATH    73 LDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPT 171
               SCOP domains d2ce0a_ A: automated matches                                                                        SCOP domains
               CATH domains 2ce0A00 A:3-101 Cytochrome c                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...hhhhh.........hhhhhhhh...hhhhhhhhhhhh............hhhh.......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:3-95 UniProt: 73-165                                                            ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2ce0 A   3 LDIQRGATLFNRACAACHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPT 101
                                    12        22        32        42        52        62        72        82        92
   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 alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CE0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC6_ARATH | Q93VA3)
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: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:0009543    chloroplast thylakoid lumen    The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
    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
        CYC6_ARATH | Q93VA3: 2ce1 2dge 2v07

(-) Related Entries Specified in the PDB File

2ce1 STRUCTURE OF REDUCED ARABIDOPSIS THALIANA CYTOCHROME 6A