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(-) Description

Title :  THE STRUCTURE OF PHYCOERYTHRIN FROM GLOEOBACTER VIOLACEUS
 
Authors :  J. W. Murray, S. Benson, J. Nield, J. Barber
Date :  10 Dec 07  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Photosynthesis, Light-Harvesting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Murray, S. Benson, J. Nield, J. Barber
The Structures Of The Phycobiliproteins Of Gloeobacter Violaceus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHYCOERYTHRIN ALPHA CHAIN
    Chains: A, C
    Organism Scientific: GLOEOBACTER VIOLACEUS
    Organism Taxid: 33072
    Other Details: PASTEUR CULTURE COLLECTION
    Strain: PCC7421
 
Molecule 2 - PHYCOERYTHRIN BETA SUBUNIT
    Chains: B, D
    Organism Scientific: GLOEOBACTER VIOLACEUS
    Organism Taxid: 33072
    Other Details: PASTEUR CULTURE COLLECTION
    Strain: PCC7421

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1MEN2Mod. Amino AcidN-METHYL ASPARAGINE
2PEB8Ligand/IonPHYCOERYTHROBILIN
3PUB2Ligand/IonPHYCOUROBILIN
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
1MEN6Mod. Amino AcidN-METHYL ASPARAGINE
2PEB24Ligand/IonPHYCOERYTHROBILIN
3PUB6Ligand/IonPHYCOUROBILIN

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:60 , ALA A:72 , GLY A:73 , LYS A:78 , LYS A:81 , CYS A:82 , ARG A:84 , ASP A:85 , HIS A:88 , TYR A:89 , TRP A:108 , LEU A:120 , LEU A:122 , ALA A:126 , TYR A:127 , HOH A:2099 , HOH A:2117 , HOH A:2154 , HOH A:2155 , HOH A:2156 , HOH A:2157 , HOH A:2158 , ILE B:67 , TYR B:74 , THR B:75 , ASN B:76 , MET B:79BINDING SITE FOR RESIDUE PEB A1082
02AC2SOFTWARELYS A:43 , GLY A:47 , ALA A:49 , ALA A:50 , VAL A:51 , GLU A:54 , TYR A:83 , ARG A:84 , ARG A:137 , ALA A:138 , CYS A:139 , ARG A:142 , ASP A:143 , HOH A:2053 , HOH A:2056 , HOH A:2135 , HOH A:2159 , HOH A:2160 , HOH A:2161 , HOH A:2162 , HOH A:2163 , HOH A:2164 , HOH A:2165 , HOH A:2166BINDING SITE FOR RESIDUE PEB A1139
03AC3SOFTWARECYS B:50 , ASP B:54 , GLY B:58 , CYS B:61 , GLU B:62 , ARG B:129 , ILE B:133 , ALA B:136 , SER B:137 , THR B:145 , ALA B:146 , SER B:147 , LYS B:148 , HOH B:2049 , HOH B:2148 , HOH B:2149 , HOH B:2150 , HOH B:2151 , HOH B:2152 , HOH B:2153BINDING SITE FOR RESIDUE PUB B1050
04AC4SOFTWAREMET B:59 , MEN B:72 , CYS 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 , LEU B:113 , LEU B:120 , PRO B:123 , ALA B:127 , HOH B:2155 , HOH B:2156 , HOH B:2157BINDING SITE FOR RESIDUE PEB B1082
05AC5SOFTWAREGLU A:25 , GLN A:28 , ASN B:35 , LYS B:36 , LEU B:38 , ASP B:39 , ILE B:142 , ASN B:144 , THR B:153 , PRO B:154 , GLY B:156 , CYS B:158 , HOH B:2158 , HOH B:2159 , HOH B:2160 , HOH B:2161 , HOH B:2162 , HOH B:2163 , HOH B:2164 , HOH B:2165 , HOH B:2166 , ARG C:33 , GLN C:147BINDING SITE FOR RESIDUE PEB B1158
06AC6SOFTWAREPHE C:60 , ALA C:72 , GLY C:73 , LYS C:78 , LYS C:81 , CYS C:82 , ARG C:84 , ASP C:85 , HIS C:88 , TYR C:89 , TRP C:108 , LEU C:120 , LEU C:122 , PRO C:123 , ALA C:126 , TYR C:127 , HOH C:2079 , HOH C:2140 , HOH C:2141 , HOH C:2142 , HOH C:2143 , ILE D:67 , THR D:75 , ASN D:76 , MET D:79 , HOH D:2060BINDING SITE FOR RESIDUE PEB C1082
07AC7SOFTWARELYS C:43 , GLY C:47 , ALA C:50 , VAL C:51 , GLU C:54 , ARG C:137 , ALA C:138 , CYS C:139 , ARG C:142 , ASP C:143 , MET C:144 , HOH C:2114 , HOH C:2124 , HOH C:2144 , HOH C:2145BINDING SITE FOR RESIDUE PEB C1139
08AC8SOFTWARECYS D:50 , ASP D:54 , GLY D:58 , CYS D:61 , GLU D:62 , ARG D:129 , ILE D:133 , ALA D:136 , SER D:137 , THR D:145 , ALA D:146 , SER D:147 , LYS D:148 , ARG D:149 , HOH D:2052 , HOH D:2143 , HOH D:2144 , HOH D:2145 , HOH D:2146BINDING SITE FOR RESIDUE PUB D1050
09AC9SOFTWAREMEN D:72 , CYS D:73 , ARG D:77 , ARG D:78 , ALA D:81 , CYS D:82 , ARG D:84 , ASP D:85 , ILE D:88 , ARG D:108 , LEU D:113 , THR D:116 , LEU D:120 , VAL D:122 , PRO D:123 , ALA D:127 , HOH D:2147 , HOH D:2148 , HOH D:2149BINDING SITE FOR RESIDUE PEB D1082
10BC1SOFTWAREARG A:33 , GLN A:147 , GLU C:25 , GLN C:28 , ASN D:35 , LYS D:36 , LEU D:38 , ASP D:39 , ILE D:142 , ASN D:143 , ASN D:144 , THR D:153 , PRO D:154 , GLN D:155 , GLY D:156 , CYS D:158 , HOH D:2124 , HOH D:2150 , HOH D:2151 , HOH D:2152 , HOH D:2153 , HOH D:2154 , HOH D:2155BINDING SITE FOR RESIDUE PEB D1158

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VJH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:140 -Pro A:141
2Ala C:140 -Pro C:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VJH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VJH)

(-) Exons   (0, 0)

(no "Exon" information available for 2VJH)

(-) 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:164
 aligned with Q7NLD7_GLOVI | Q7NLD7 from UniProtKB/TrEMBL  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         Q7NLD7_GLOVI     1 MKSVVTTVLAAADAAGRFPSGSDLESVQGNIQRSAARLEAAEKLAAGHAAVVKEAGDVVFKKYPYLKTAGEAGDSAEKVAKCYRDIDHYMRLINYCLVVGGTGPLDEWGISGAREVYRALNLPTAAYVAAFQYTRDRACAPRDMGPQALTEFRSYLDYVINALS 164
               SCOP domains d2vjha_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjh A   1 MKSVVTTVLAAADAAGRFPSGSDLESVQGNIQRSAARLEAAEKLAAGHAAVVKEAGDVVFKKYPYLKTAGEAGDSAEKVAKCYRDIDHYMRLINYCLVVGGTGPLDEWGISGAREVYRALNLPTAAYVAAFQYTRDRACAPRDMGPQALTEFRSYLDYVINALS 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with Q7NLD6_GLOVI | Q7NLD6 from UniProtKB/TrEMBL  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
         Q7NLD6_GLOVI     1 MLDAFSKAVVSADQKTGYIGGAELAALKTYIANGNKRLDAVNAITSNASCIVSDAVSGMICENPGLISAGGNCYTNRRMAACLRDGEIVLRYVTYALLAGDASVLEDRCLNGLKETYMALGVPIPSAIRAVSIMKASAVAFINNTASKRKIETPQGDCAALASEAGSYFDMAASALR 177
               SCOP domains d2vjhb_ B: automated matches                                                                                                                                                      SCOP domains
               CATH domains 2vjhB00 B:1-177 Phycocyanins                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjh B   1 MLDAFSKAVVSADQKTGYIGGAELAALKTYIANGNKRLDAVNAITSNASCIVSDAVSGMICENPGLISAGGnCYTNRRMAACLRDGEIVLRYVTYALLAGDASVLEDRCLNGLKETYMALGVPIPSAIRAVSIMKASAVAFINNTASKRKIETPQGDCAALASEAGSYFDMAASALR 177
                                    10        20        30        40        50        60        70 |      80        90       100       110       120       130       140       150       160       170       
                                                                                                  72-MEN                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:164
 aligned with Q7NLD7_GLOVI | Q7NLD7 from UniProtKB/TrEMBL  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         Q7NLD7_GLOVI     1 MKSVVTTVLAAADAAGRFPSGSDLESVQGNIQRSAARLEAAEKLAAGHAAVVKEAGDVVFKKYPYLKTAGEAGDSAEKVAKCYRDIDHYMRLINYCLVVGGTGPLDEWGISGAREVYRALNLPTAAYVAAFQYTRDRACAPRDMGPQALTEFRSYLDYVINALS 164
               SCOP domains d2vjhc_ C: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjh C   1 MKSVVTTVLAAADAAGRFPSGSDLESVQGNIQRSAARLEAAEKLAAGHAAVVKEAGDVVFKKYPYLKTAGEAGDSAEKVAKCYRDIDHYMRLINYCLVVGGTGPLDEWGISGAREVYRALNLPTAAYVAAFQYTRDRACAPRDMGPQALTEFRSYLDYVINALS 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain D from PDB  Type:PROTEIN  Length:177
 aligned with Q7NLD6_GLOVI | Q7NLD6 from UniProtKB/TrEMBL  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
         Q7NLD6_GLOVI     1 MLDAFSKAVVSADQKTGYIGGAELAALKTYIANGNKRLDAVNAITSNASCIVSDAVSGMICENPGLISAGGNCYTNRRMAACLRDGEIVLRYVTYALLAGDASVLEDRCLNGLKETYMALGVPIPSAIRAVSIMKASAVAFINNTASKRKIETPQGDCAALASEAGSYFDMAASALR 177
               SCOP domains d2vjhd_ D: automated matches                                                                                                                                                      SCOP domains
               CATH domains 2vjhD00 D:1-177 Phycocyanins                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjh D   1 MLDAFSKAVVSADQKTGYIGGAELAALKTYIANGNKRLDAVNAITSNASCIVSDAVSGMICENPGLISAGGnCYTNRRMAACLRDGEIVLRYVTYALLAGDASVLEDRCLNGLKETYMALGVPIPSAIRAVSIMKASAVAFINNTASKRKIETPQGDCAALASEAGSYFDMAASALR 177
                                    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  (1, 4)

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 2VJH)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q7NLD7_GLOVI | Q7NLD7)
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,D   (Q7NLD6_GLOVI | Q7NLD6)
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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  2vjh
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 Related Entries

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