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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF C-PHYCOCYANIN FROM THERMOSYNECHOCOCCUS ELONGATUS
 
Authors :  R. Fromme, D. Brune, P. Fromme
Date :  09 Dec 09  (Deposition) - 29 Dec 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (6x)
Keywords :  Photosynthesis, Photosystem Ii, Light Harvesting Proteins, Thermostability, Bile Pigment, Chloroplast, Chromophore, Electron Transport, Membrane, Phycobilisome, Plastid, Thylakoid, Transport, Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fromme, D. Brune, P. Fromme
The 3 Dimensional Structure Of C-Phycocyanin At 1. 35 A Resolution
To Be Published 2010
PubMed: search

(-) Compounds

Molecule 1 - C-PHYCOCYANIN ALPHA CHAIN
    Chains: A
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 197221
    Other Details: FORMER NAME SYNECHOCOCCUS ELONGATUS
    Strain: BP-1
 
Molecule 2 - C-PHYCOCYANIN BETA CHAIN
    Chains: B
    Engineered: YES
    Gene: CPCB, TLR1957
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 197221
    Strain: BP-1

 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. Amino AcidN-METHYL ASPARAGINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CYC18Ligand/IonPHYCOCYANOBILIN
2MEN6Mod. Amino AcidN-METHYL ASPARAGINE

(-) 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 , 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 , LEU A:124 , TRP A:128 , TYR A:129 , HOH A:195 , HOH A:199 , HOH A:245 , HOH A:274 , HOH A:349 , ARG B:57 , ILE B:67 , THR B:75 , ASN B:76 , HOH B:203BINDING SITE FOR RESIDUE CYC A 484
2AC2SOFTWARELEU B:59 , MEN B:72 , ALA B:73 , ARG B:77 , ARG B:78 , ALA B:81 , CYS B:82 , ARG B:84 , ASP B:85 , ILE B:88 , ARG B:108 , CYS B:109 , LEU B:113 , LEU B:120 , THR B:122 , HOH B:265 , HOH B:296 , HOH B:310 , HOH B:335 , HOH B:364 , HOH B:580 , HOH B:631BINDING SITE FOR RESIDUE CYC B 584
3AC3SOFTWAREASN A:21 , LEU A:24 , ASP A:28 , ARG A:33 , GLN A:145 , HOH A:206 , ASN B:35 , LYS B:36 , ASP B:39 , ALA B:142 , ASN B:143 , ILE B:148 , THR B:149 , PRO B:150 , GLY B:151 , CYS B:153 , HOH B:239 , HOH B:287 , HOH B:303 , HOH B:308 , HOH B:320 , HOH B:403 , HOH B:415 , HOH B:576 , HOH B:605 , HOH B:633BINDING SITE FOR RESIDUE CYC B 555

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L0F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L0F)

(-) Exons   (0, 0)

(no "Exon" information available for 3L0F)

(-) 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 PHCA_THEEB | P50032 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           PHCA_THEEB     1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMVTYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 162
               SCOP domains d3l0fa_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----Phycobilisome-3l0fA01 A:6-162                                                                                                                                 Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l0f A   1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMVTYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


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 d3l0fb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Phycobilisome-3l0fB01 B:6-172                                                                                                                                           Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0f B   1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGnAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 172
                                    10        20        30        40        50        60        70 |      80        90       100       110       120       130       140       150       160       170  
                                                                                                  72-MEN
   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  (0, 0)

(no "CATH Domain" information available for 3L0F)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (7, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHCA_THEEB | P50032)
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   (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
        PHCA_THEEB | P50032: 1jbo 1ktp 4q70 4z8k 4ziz 5uvk
        PHCB_THEEB | P50033: 1i7y 1jbo 1ktp 1on7 4q70 4z8k 4ziz 5uvk

(-) Related Entries Specified in the PDB File

1f99 POLYSIPHONIA AT 2.4 A
1jb0 SYNECHOCOCCUS ELONGATUS AT 1.45A
1ktp SYNECHOCOCCUS VULCANUS AT 1.6 A
1phn CYANIDIUM CALDARIUM AT 1.65 A
2bv8 GRACILARIA CHILENSIS AT 2 A
3brp GALDIERIA SULPHURARIA AT 1.85