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(-) Description

Title :  CRYSTAL STRUCTURE OF C-PHYCOCYANIN OF SYNECHOCOCCUS VULCANUS AT 2.5 ANGSTROMS.
 
Authors :  N. Adir, E. Dobrovetsky, N. Lerner
Date :  11 Mar 01  (Deposition) - 28 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (6x)
Keywords :  Cyanobacteria, Photosynthesis, Photosystem Ii, Light Harvesting Proteins, Thermostability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Adir, Y. Dobrovetsky, N. Lerner
Structure Of C-Phycocyanin From The Thermophilic Cyanobacterium Synechococcus Vulcanus At 2. 5 A: Structural Implications For Thermal Stability In Phycobilisome Assembly.
J. Mol. Biol. V. 313 71 2001
PubMed-ID: 11601847  |  Reference-DOI: 10.1006/JMBI.2001.5030

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (6x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
2MEN1Mod. ResidueN-METHYL ASPARAGINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CYC18Ligand/IonPHYCOCYANOBILIN
2MEN6Mod. ResidueN-METHYL ASPARAGINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:66 , SER A:72 , GLN A:73 , TYR A:74 , ALA A:75 , GLY A:80 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:90 , TYR A:110 , ILE A:118 , PHE A:122 , TRP A:128 , TYR A:129 , HOH A:187 , HOH A:188 , HOH A:219 , ARG B:57 , THR B:77 , ASN B:78BINDING SITE FOR RESIDUE CYC A 184
2AC2SOFTWAREASN B:72 , THR B:124 , CYC B:284BINDING SITE FOR RESIDUE MEN B 272
3AC3SOFTWARELEU B:66 , ASN B:72 , ARG B:79 , ARG B:80 , ALA B:83 , CYS B:84 , ARG B:86 , ASP B:87 , ILE B:90 , TYR B:94 , ARG B:110 , LEU B:115 , LEU B:122 , THR B:124 , SER B:128 , MEN B:272BINDING SITE FOR RESIDUE CYC B 284
4AC4SOFTWAREASN A:21 , ASP A:28 , ARG A:33 , GLN A:147 , ASN B:35 , ASP B:39 , ALA B:144 , ASN B:145 , ASP B:146 , ILE B:150 , THR B:151 , PRO B:152 , GLY B:153 , CYS B:155 , HOH B:363 , HOH B:366BINDING SITE FOR RESIDUE CYC B 355

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I7Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I7Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1I7Y)

(-) 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 d1i7ya_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1i7yA00 A:1-174 Phycocyanins                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1i7y 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 d1i7yb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1i7yB00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i7y 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 d1i7yb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1i7yB00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i7y 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  (0, 0)

(no "Pfam Domain" information available for 1I7Y)

(-) 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   (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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHCB_THEEB | P50033: 1jbo 1ktp 1on7 3l0f 4q70 4z8k 4ziz 5uvk
UniProtKB/TrEMBL
        Q71RW8_THEVL | Q71RW8: 1on7 3o18 3o2c 4gxe 4gy3 4n6s
        Q9AM02_THEVL | Q9AM02: 1on7 3o18 3o2c 4gxe 4gy3 4n6s

(-) Related Entries Specified in the PDB File

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