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(-) Description

Title :  UNMETHYLATED FORM OF C-PHYCOCYANIN FROM THEMOSYNECHOCOCCUS VULCANUS AT 2.7A
 
Authors :  N. Adir, N. Lerner
Date :  27 Feb 03  (Deposition) - 29 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Photosynthesis, Antenna, Phycobilisome, Cyanobacteria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Adir, N. Lerner
The Crystal Structure Of A Novel Unmethylated Form Of C-Phycocyanin, A Possible Connector Between Cores And Rods In Pycobilisomes
J. Biol. Chem. V. 278 25926 2003
PubMed-ID: 12709431  |  Reference-DOI: 10.1074/JBC.M302838200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-PHYCOCYANIN ALPHA SUBUNIT
    Chains: A
    Organism Scientific: THERMOSYNECHOCOCCUS VULCANUS
    Organism Taxid: 32053
    Other Details: PHYCOBILISOME
 
Molecule 2 - C-PHYCOCYANIN BETA SUBUNIT
    Chains: B
    Organism Scientific: THERMOSYNECHOCOCCUS VULCANUS
    Organism Taxid: 32053
    Other Details: PHYCOBILISOME

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1CYC9Ligand/IonPHYCOCYANOBILIN

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:59 , THR A:66 , SER A:72 , GLN A:73 , TYR A:74 , ALA A:75 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:110 , PHE A:122 , TRP A:128 , TYR A:129 , ARG B:57 , ILE B:67 , TYR B:76 , THR B:77 , ASN B:78BINDING SITE FOR RESIDUE CYC A 484
2AC2SOFTWARELEU B:66 , ASN B:72 , ALA B:75 , ARG B:79 , ARG B:80 , CYS B:84 , ARG B:86 , ASP B:87 , ILE B:90 , ARG B:110 , LEU B:115 , TYR B:119 , LEU B:122 , THR B:124 , SER B:128BINDING SITE FOR RESIDUE CYC B 584
3AC3SOFTWAREGLN A:25 , ASP A:28 , HOH A:489 , ASN B:35 , ASP B:39 , ASN B:145 , ASP B:146 , ILE B:150 , THR B:151 , PRO B:152 , GLY B:153 , CYS B:155 , SER B:156 , SER B:160 , ALA B:163BINDING SITE FOR RESIDUE CYC B 555

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ON7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ON7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ON7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ON7)

(-) Exons   (0, 0)

(no "Exon" information available for 1ON7)

(-) 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:162
 aligned with Q9AM02_THEVL | Q9AM02 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q9AM02_THEVL     1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMITYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 162
               SCOP domains d1on7a_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1on7A00 A:1-174 Phycocyanins                                                                                                                                       CATH domains
               Pfam domains -----Phycobilisome-1on7A01 A:6-174                                                                                                                                 Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1on7 A   1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMITYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      162       172  
                                                                                                                                                                     140|    150|             
                                                                                                                                                                      143     161             


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with PHCB_THEEB | P50033 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           PHCB_THEEB     1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 172
               SCOP domains d1on7b_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1on7B00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains -----Phycobilisome-1on7B01 B:6-174                                                                                                                                           Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1on7 B   1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72|                                                                                                   
                                                                                                   75                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q71RW8_THEVL | Q71RW8 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q71RW8_THEVL     1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 172
               SCOP domains d1on7b_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1on7B00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains -----Phycobilisome-1on7B01 B:6-174                                                                                                                                           Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1on7 B   1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72|                                                                                                   
                                                                                                   75
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (7, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9AM02_THEVL | Q9AM02)
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.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.

Chain B   (Q71RW8_THEVL | Q71RW8)
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.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.

Chain B   (PHCB_THEEB | P50033)
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.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
    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.
    GO:0042651    thylakoid membrane    The pigmented membrane of any thylakoid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHCB_THEEB | P50033: 1i7y 1jbo 1ktp 3l0f 4q70 4z8k 4ziz 5uvk
UniProtKB/TrEMBL
        Q71RW8_THEVL | Q71RW8: 1i7y 3o18 3o2c 4gxe 4gy3 4n6s
        Q9AM02_THEVL | Q9AM02: 1i7y 3o18 3o2c 4gxe 4gy3 4n6s

(-) Related Entries Specified in the PDB File

1i7y 1ktp