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(-) Description

Title :  STRUCTURE OF THE NOVEL 14 KDA FRAGMENT OF ALPHA-SUBUNIT OF PHYCOERYTHRIN FROM THE STARVING CYANOBACTERIUM PHORMIDIUM TENUE
 
Authors :  B. R. Soni, M. I. Hasan, A. Parmar, A. S. Ethayathulla, R. P. Kumar, N. K. S M. Sinha, P. Kaur, S. Yadav, S. Sharma, D. Madamwar, T. P. Singh
Date :  06 May 10  (Deposition) - 30 Jun 10  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phycoerythrin, Cyanobacterium, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Soni, M. I. Hasan, A. Parmar, A. S. Ethayathulla, R. P. Kumar, N. K. Singh, M. Sinha, P. Kaur, S. Yadav, S. Sharma, D. Madamwar, T. P. Singh
Structure Of The Novel 14Kda Fragment Of Alpha-Subunit Of Phycoerythrin From The Starving Cyanobacterium Phormidium Tenue.
J. Struct. Biol. V. 171 247 2010
PubMed-ID: 20546902  |  Reference-DOI: 10.1016/J.JSB.2010.05.008

(-) Compounds

Molecule 1 - PHYCOERYTHRIN
    Chains: A, B
    Organism Scientific: PHORMIDIUM TENUE
    Organism Taxid: 126344

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CYC4Ligand/IonPHYCOCYANOBILIN
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CYC2Ligand/IonPHYCOCYANOBILIN
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CYC2Ligand/IonPHYCOCYANOBILIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:1060 , ASN A:1066 , ALA A:1072 , GLY A:1073 , LYS A:1078 , LYS A:1081 , CYS A:1082 , ARG A:1084 , ASP A:1085 , HIS A:1088 , TRP A:1108 , TYR A:1117 , LEU A:1120 , LEU A:1122 , ALA A:1126 , TYR A:1127 , HOH A:3119BINDING SITE FOR RESIDUE CYC A 3001
2AC2SOFTWARELEU A:1044 , ASN A:1047 , ALA A:1050 , GLU A:1054 , ARG A:1137 , LEU A:1138 , CYS A:1139 , ARG A:1142 , PHE A:1152 , HOH A:3142BINDING SITE FOR RESIDUE CYC A 3002
3AC3SOFTWAREALA B:2072 , GLY B:2073 , LYS B:2078 , LYS B:2081 , CYS B:2082 , ASP B:2085 , HIS B:2088 , TYR B:2089 , LEU B:2120 , ALA B:2126 , TYR B:2127BINDING SITE FOR RESIDUE CYC B 3003
4AC4SOFTWARELYS B:2043 , LEU B:2044 , ASN B:2047 , VAL B:2051 , GLU B:2054 , ARG B:2137 , LEU B:2138 , CYS B:2139 , ARG B:2142 , ASP B:2143BINDING SITE FOR RESIDUE CYC B 3004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MWN)

(-) 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:133
 aligned with A4L2N4_9CYAN | A4L2N4 from UniProtKB/TrEMBL  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
        A4L2N4_9CYAN      1 QRAAARLEAAEKLGSNLEAVTKEAGDACFSKYSYNKNPGEAGENQEKVDKCYRDILHYMRLINYTLVVGGTGPLDEWGIAGAREVYRTLNLPSAAYIAAFTFTRDRLCAPRDMSAQAGTEFSTALDYLINSLS  133
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh...............hhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mwn A 1032 QRAAARLEAAEKLGSNHEAVVKEAGDACFSKYGYNKNPGEAGENQEKINKCYRDIDHYMRLINYTLVVGGTGPLDEWGIAGAREVYRTLNLPSAAYIAAFVFTRDRLCAPRDMSAQAGVEFCTALDYLINSLS 1164
                                  1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161   


Chain A from PDB  Type:PROTEIN  Length:133
 aligned with PHEA_POLUR | P84861 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:133
                                    41        51        61        71        81        91       101       111       121       131       141       151       161   
          PHEA_POLUR     32 QRAAARLEAAEKLGSNHEAVVKEAGDACFSKYGYNKNPGEAGENQEKINKCYRDIDHYMRLINYTLVVGGTGPLDEWGIAGAREVYRTLNLPSAAYIAAFVFTRDRLCIPRDMSAQAGVEFCTALDYLINSLS  164
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh...............hhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mwn A 1032 QRAAARLEAAEKLGSNHEAVVKEAGDACFSKYGYNKNPGEAGENQEKINKCYRDIDHYMRLINYTLVVGGTGPLDEWGIAGAREVYRTLNLPSAAYIAAFVFTRDRLCAPRDMSAQAGVEFCTALDYLINSLS 1164
                                  1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161   


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with A4L2N4_9CYAN | A4L2N4 from UniProtKB/TrEMBL  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
        A4L2N4_9CYAN      1 QRAAARLEAAEKLGSNLEAVTKEAGDACFSKYSYNKNPGEAGENQEKVDKCYRDILHYMRLINYTLVVGGTGPLDEWGIAGAREVYRTLNLPSAAYIAAFTFTRDRLCAPRDMSAQAGTEFSTALDYLINSLS  133
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mwn B 2032 QRAAARLEAAEKLGSNHEAVVKEAGDACFSKYGYNKNPGEAGENQEKINKCYRDIDHYMRLINYTLVVGGTGPLDEWGIAGAREVYRTLNLPSAAYIAAFVFTRDRLCAPRDMSAQAGVEFCTALDYLINSLS 2164
                                  2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161
   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  (0, 0)

(no "SCOP Domain" information available for 3MWN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MWN)

(-) Gene Ontology  (9, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHEA_POLUR | P84861)
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 A,B   (A4L2N4_9CYAN | A4L2N4)
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

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        PHEA_POLUR | P84861: 1lia

(-) Related Entries Specified in the PDB File

1lia CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA AT 2.8 A RESOLUTION