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(-) Description

Title :  CRYSTAL STRUCTURE OF PSBP PROTEIN IN THE OXYGEN-EVOLVING COMPLEX OF PHOTOSYSTEM II FROM HIGHER PLANTS
 
Authors :  K. Ifuku, T. Nakatsu, H. Kato, F. Sato, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Oct 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ifuku, T. Nakatsu, H. Kato, F. Sato
Crystal Structure Of The Psbp Protein Of Photosystem Ii From Nicotiana Tabacum
Embo Rep. V. 5 362 2004
PubMed-ID: 15031714  |  Reference-DOI: 10.1038/SJ.EMBOR.7400113
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 23-KDA POLYPEPTIDE OF PHOTOSYSTEM II OXYGEN- EVOLVING COMPLEX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21D
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 10-186
    Gene: PSBP
    Organism Common: COMMON TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097
    Synonym: OXYGEN-EVOLVING COMPLEX 23-KDA PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GLC2Ligand/IonALPHA-D-GLUCOSE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GLC1Ligand/IonALPHA-D-GLUCOSE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GLC1Ligand/IonALPHA-D-GLUCOSE
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:33 , TRP A:34 , ASP A:51 , ARG A:167 , PHE A:175 , HOH A:1220 , HOH A:1228 , HOH A:1248 , HOH A:1291 , SER B:117 , THR B:118 , HOH B:1219 , HOH B:1222BINDING SITE FOR RESIDUE GLC A 1203
2AC2SOFTWARESER A:117 , THR A:118 , HOH A:1214 , HOH A:1215 , LYS B:33 , TRP B:34 , ASP B:51 , ARG B:167 , PHE B:175 , HOH B:1214 , HOH B:1226 , HOH B:1284BINDING SITE FOR RESIDUE GLC B 1204
3AC3SOFTWARELYS B:170 , GLY B:171 , ALA B:172 , LYS B:173 , LYS B:174 , HOH B:1231 , HOH B:1408 , HOH B:1434BINDING SITE FOR RESIDUE SO4 B 1201
4AC4SOFTWARELYS A:170 , GLY A:171 , ALA A:172 , LYS A:173 , LYS A:174 , HOH A:1240 , HOH A:1309BINDING SITE FOR RESIDUE SO4 A 1202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V2B)

(-) Exons   (0, 0)

(no "Exon" information available for 1V2B)

(-) Sequences/Alignments

Asymmetric 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:148
 aligned with PSBP2_TOBAC | P18212 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:171
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
          PSBP2_TOBAC    95 TDFQTYNGDGFKLQIPSKWNPNKEVEYPGQVLRFEDNFDATSNVIVAITPTDKKSITDFGSPEQFLSQVDYLLGRQAYSGKTDSEGGFESDAVAIANVLETSSAEVGGKPYYYLSVLTRTADGNEGGKHQLITATVNDGKLYICKAQAGDKRWFKGAKKFVENTATSFSLA 265
               SCOP domains d1v2ba_ A: Oxygen-evolving enhancer protein PsbP                                                                                                                            SCOP domains
               CATH domains 1v2bA00 A:16-186 Protein Transport Mog1p; Chain A                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee...ee........eeeeeee..eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhh------------------...eeeeeeeeeeee..eeeeeeeeeee.-----..eeeeeeeeee..eeeeeeeeee.hhh....hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v2b A  16 TDFQTYNGDGFKLQIPSKWNPNKEVEYPGQVLRFEDNFDATSNVIVAITPTDKKSITDFGSPEQFLSQVDYLL------------------AVAIANVLETSTAEVGGKQYYYLSILTRT-----GGKHQLVTATVNDGKLYICKAQAGDKRWFKGAKKFVENTATSFSLA 186
                                    25        35        45        55        65        75        85  |      -         - |     115       125       135     | 145       155       165       175       185 
                                                                                                   88                107                         135   141                                             


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with PSBP2_TOBAC | P18212 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:171
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
          PSBP2_TOBAC    95 TDFQTYNGDGFKLQIPSKWNPNKEVEYPGQVLRFEDNFDATSNVIVAITPTDKKSITDFGSPEQFLSQVDYLLGRQAYSGKTDSEGGFESDAVAIANVLETSSAEVGGKPYYYLSVLTRTADGNEGGKHQLITATVNDGKLYICKAQAGDKRWFKGAKKFVENTATSFSLA 265
               SCOP domains d1v2bb_ B: Oxygen-evolving enhancer protein PsbP                                                                                                                            SCOP domains
               CATH domains 1v2bB00 B:16-186 Protein Transport Mog1p; Chain A                                                                                                                           CATH domains
           Pfam domains (1) PsbP-1v2bB01 B:16-186                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) PsbP-1v2bB02 B:16-186                                                                                                                                                       Pfam domains (2)
         Sec.struct. author ..eeeee...eeeeee...ee........eeeeeee..eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.-----------------..eeeeeeeeeeee..eeeeeeeeeee...---..eeeeeeeeee..eeeeeeeeee.hhh....hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v2b B  16 TDFQTYNGDGFKLQIPSKWNPNKEVEYPGQVLRFEDNFDATSNVIVAITPTDKKSITDFGSPEQFLSQVDYLLGR-----------------VAIANVLETSTAEVGGKQYYYLSILTRTAD---GGKHQLVTATVNDGKLYICKAQAGDKRWFKGAKKFVENTATSFSLA 186
                                    25        35        45        55        65        75        85    |    -         -  |    115       125       135 |   | 145       155       165       175       185 
                                                                                                     90               108                          137 141
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: PsbP] (3)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PSBP2_TOBAC | P18212)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
biological process
    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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009523    photosystem II    A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center.
    GO:0009654    photosystem II oxygen evolving complex    A complex, composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins, that catalyzes the splitting of water to O2 and 4 H+. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ).
    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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