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(-) Description

Title :  STRUCTURE OF PHYCOCYANIN FROM CYANIDIUM CALDARIUM AT 1.65A RESOLUTION
 
Authors :  B. Stec, R. F. Troxler, M. M. Teeter
Date :  21 Jun 95  (Deposition) - 17 Sep 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (6x)
Biol. Unit 3:  A,B  (3x)
Biol. Unit 4:  A (2x),B (2x)
Biol. Unit 5:  A,B  (2x)
Keywords :  Phycocyanin, Phycobilisome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Stec, R. F. Troxler, M. M. Teeter
Crystal Structure Of C-Phycocyanin From Cyanidium Caldarium Provides A New Perspective On Phycobilisome Assembly.
Biophys. J. V. 76 2912 1999
PubMed-ID: 10354419
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHYCOCYANIN
    Chains: A
    Fragment: CHAIN A IS THE ALPHA CHAIN, CHAIN B IS THE BETA CHAIN
    Organism Scientific: CYANIDIUM CALDARIUM
    Organism Taxid: 2771
 
Molecule 2 - PHYCOCYANIN
    Chains: B
    Fragment: CHAIN A IS THE ALPHA CHAIN, CHAIN B IS THE BETA CHAIN
    Organism Scientific: CYANIDIUM CALDARIUM
    Organism Taxid: 2771

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (6x): AB
Biological Unit 3 (3x): AB
Biological Unit 4 (2x): A (2x)B (2x)
Biological Unit 5 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CYC2Ligand/IonPHYCOCYANOBILIN
2MEN1Mod. Amino AcidN-METHYL ASPARAGINE
3PEB1Ligand/IonPHYCOERYTHROBILIN
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CYC2Ligand/IonPHYCOCYANOBILIN
2MEN1Mod. Amino AcidN-METHYL ASPARAGINE
3PEB1Ligand/IonPHYCOERYTHROBILIN
Biological Unit 2 (3, 24)
No.NameCountTypeFull Name
1CYC12Ligand/IonPHYCOCYANOBILIN
2MEN6Mod. Amino AcidN-METHYL ASPARAGINE
3PEB6Ligand/IonPHYCOERYTHROBILIN
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1CYC6Ligand/IonPHYCOCYANOBILIN
2MEN3Mod. Amino AcidN-METHYL ASPARAGINE
3PEB3Ligand/IonPHYCOERYTHROBILIN
Biological Unit 4 (3, 6)
No.NameCountTypeFull Name
1CYC2Ligand/IonPHYCOCYANOBILIN
2MEN2Mod. Amino AcidN-METHYL ASPARAGINE
3PEB2Ligand/IonPHYCOERYTHROBILIN
Biological Unit 5 (3, 8)
No.NameCountTypeFull Name
1CYC4Ligand/IonPHYCOCYANOBILIN
2MEN2Mod. Amino AcidN-METHYL ASPARAGINE
3PEB2Ligand/IonPHYCOERYTHROBILIN

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:59 , THR A:66 , PRO 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:277 , ARG B:57 , ILE B:67 , THR B:77 , ASN B:78 , HOH B:215 , HOH B:216 , HOH B:218 , HOH B:329BINDING SITE FOR RESIDUE CYC A 184
2AC2SOFTWAREASN A:28 , ARG A:33 , GLN A:147 , ASN A:150 , HOH A:195 , HOH A:207 , HOH A:343 , HOH A:419 , ASN B:35 , LYS B:36 , ASP B:39 , VAL B:40 , ASP B:146 , ILE B:150 , THR B:151 , THR B:152 , GLY B:153 , CYS B:155 , HOH B:187 , HOH B:189 , HOH B:395BINDING SITE FOR RESIDUE CYC B 183
3AC3SOFTWARELEU B:66 , MEN B:72 , ALA B:75 , ARG B:79 , ARG B:80 , ALA B:83 , CYS B:84 , ARG B:86 , ASP B:87 , ILE B:90 , LEU B:115 , LEU B:122 , HOH B:352BINDING SITE FOR RESIDUE PEB B 182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PHN)

(-) 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_GALSU | P00306 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_GALSU     1 MKTPITEAIAAADNQGRFLSNTELQAVNGRYQRAAASLEAARSLTSNAERLINGAAQAVYSKFPYTSQMPGPQYASSAVGKAKCARDIGYYLRMVTYCLVVGGTGPMDEYLIAGLEEINRTFDLSPSWYVEALNYIKANHGLSGQAANEANTYIDYAINALS 162
               SCOP domains d1phna_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1phnA00 A:1-174 Phycocyanins                                                                                                                                       CATH domains
               Pfam domains -----Phycobilisome-1phnA01 A:6-174                                                                                                                                 Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1phn A   1 MKTPITEAIAAADNQGRFLSNTELQAVNGRYQRAAASLEAARSLTSNAERLINGAAQAVYSKFPYTSQMPGPQYASSAVGKAKCARDIGYYLRMVTYCLVVGGTGPMDEYLIAGLEEINRTFDLSPSWYVEALNYIKANHGLSGQAANEANTYIDYAINALS 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_GALSU | P00311 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_GALSU     1 MLDAFAKVVAQADARGEFLSNTQLDALSKMVSEGNKRLDVVNRITSNASAIVTNAARALFSEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVSYAIIAGDSSILDDRCLNGLRETYQALGVPGASVAVGIEKMKDSAIAIANDPSGITTGDCSALMAEVGTYFDRAATAVQ 172
               SCOP domains d1phnb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1phnB00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains -----Phycobilisome-1phnB01 B:6-174                                                                                                                                           Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1phn B   1 MLDAFAKVVAQADARGEFLSNTQLDALSKMVSEGNKRLDVVNRITSNASAIVTNAARALFSEQPQLIQPGGnAYTNRRMAACLRDMEIILRYVSYAIIAGDSSILDDRCLNGLRETYQALGVPGASVAVGIEKMKDSAIAIANDPSGITTGDCSALMAEVGTYFDRAATAVQ 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72-MEN                                                                                                
                                                                                                   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  (9, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHCA_GALSU | P00306)
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: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: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: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.

Chain B   (PHCB_GALSU | P00311)
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: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: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: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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  1phn
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  PHCB_GALSU | P00311
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHCA_GALSU | P00306: 3brp 3kvs
        PHCB_GALSU | P00311: 3brp 3kvs

(-) Related Entries Specified in the PDB File

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