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(-) Description

Title :  CRYSTAL STRUCTURE OF ALLOPHYCOCYANIN
 
Authors :  D. C. Liang, J. Y. Liu, T. Jiang, J. P. Zhang, W. R. Chang
Date :  18 Dec 01  (Deposition) - 18 Dec 02  (Release) - 07 Oct 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (6x)
Keywords :  Helix-Turn-Helix, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Liu, T. Jiang, J. P. Zhang, D. C. Liang
Crystal Structure Of Allophycocyanin From Red Algae Porphyra Yezoensis At 2. 2 A Resolution
J. Biol. Chem. V. 274 16945 1999
PubMed-ID: 10358042  |  Reference-DOI: 10.1074/JBC.274.24.16945
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALLOPHYCOCYANIN
    Chains: A
    Organism Scientific: PORPHYRA YEZOENSIS
    Organism Taxid: 2788
 
Molecule 2 - ALLOPHYCOCYANIN
    Chains: B
    Organism Scientific: PORPHYRA YEZOENSIS
    Organism Taxid: 2788

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CYC2Ligand/IonPHYCOCYANOBILIN
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CYC12Ligand/IonPHYCOCYANOBILIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:72 , MET A:80 , THR A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:90 , TYR A:91 , ILE A:110 , MET A:118 , TYR A:119 , ALA A:128 , HOH A:246 , LEU B:61 , TYR B:62 , THR B:67 , THR B:77BINDING SITE FOR RESIDUE CYC A 184
2AC2SOFTWAREILE B:66 , ASN B:72 , ARG B:79 , ARG B:80 , CYS B:84 , ARG B:86 , ASP B:87 , TYR B:90 , TYR B:94 , ARG B:110 , LEU B:122 , VAL B:124 , PRO B:125 , THR B:129 , HOH B:196BINDING SITE FOR RESIDUE CYC B 184

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KN1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KN1)

(-) Exons   (0, 0)

(no "Exon" information available for 1KN1)

(-) 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:160
 aligned with PHAA_PYRYE | P59856 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
           PHAA_PYRYE     2 SIVTKSIVNADAEARYLSPGELDRIKSFVLSGQRRLRIAQILTDNRERIVKQGGQQLFQKRPDVVSPGGNAYGEEMTATCLRDLDYYLRLVTYGIVAGDVTPIEEIGLVGVKEMYNSLGTPISGVAEGVKCMKSVACSLLAGEDSAEAGFYFDYTLGAMQ 161
               SCOP domains d1kn1a_ A: Allophycocyanin alpha subunit                                                                                                                         SCOP domains
               CATH domains 1kn1A00 A:3-174 Phycocyanins                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kn1 A   3 SIVTKSIVNADAEARYLSPGELDRIKSFVLSGARRVRIAQTLTENRERIVKQAGDQLFQKRPDVVSPGGNAYGEEMTATCLRDLDYYLRLVTYGIVSGDVTPIEEIGLVGVREMYKSLGTPISAVAEGVKCMKSVASSLLSGEDSAEAGFYFDYVVGAMQ 174
                                    12        22        32        42        52        62        72|       84        94       104       114       124       134       144     ||164       174
                                                                                                72|                                                                        150|             
                                                                                                 75                                                                         161             


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with APCB_PYRYE | P59857 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           APCB_PYRYE     1 MQDAITSVINAADVQGKYLDDSSVEKLRGYFQTGELRVRAAATIAANAATIIKESVAKSLLYSDITRPGGNMYTTRRYAACIRDLDYYLRYATYGMLAGDPSILEERVLNGLKETYNSLGVPIGATIQAILAMKEVTISLVGPDAGKEMGLYFDYICSGLS 161
               SCOP domains d1kn1b_ B: Allophycocyanin beta subunit                                                                                                                           SCOP domains
               CATH domains 1kn1B00 B:1-174 Phycocyanins                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kn1 B   1 MQDAITSVINSSDVQGKYLDSSAIEKLKGYFQTGELRVRAATTIAANAANIIKEAVAKSLLYSDITRPGGNMYTTRRYAACIRDLDYYLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPIGATIQAIQAMKEVTSGLVGPDAGKEMGLYFDYICSGLS 174
                                    10        20        30        40        50        60 ||     71||      83        93       103       113       123       133       143      |163       173 
                                                                                        62|      72|                                                                        150|             
                                                                                         64       75                                                                         161
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1KN1)

(-) Gene Ontology  (9, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHAA_PYRYE | P59856)
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   (APCB_PYRYE | P59857)
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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