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(-) Description

Title :  CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS
 
Authors :  C. Contreras-Martel, P. Legrand, C. Piras, X. Vernede, J. Martinez- Oyanedel, M. Bunster, J. C. Fontecilla-Camps
Date :  09 May 00  (Deposition) - 22 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,G,H,K,L
Biol. Unit 1:  A,B,G,H,K,L  (1x)
Biol. Unit 2:  A,B,G,H,K,L  (3x)
Keywords :  R-Phycoerythrin, Macroseeding, Twin, Protein Structure, Sequences, Phycobiliprotein, Red Algae, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Contreras-Martel, J. Martinez-Oyanedel, M. Bunster, P. Legrand, C. Piras, X. Vernede, J. C. Fontecilla-Camps
Crystallization And 2. 2 A Resolution Structure Of R-Phycoerythrin From Gracilaria Chilensis: A Case Of Perfect Hemihedral Twinning.
Acta Crystallogr. , Sect. D V. 57 52 2001
PubMed-ID: 11134927  |  Reference-DOI: 10.1107/S0907444900015274
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - R-PHYCOERYTHRIN
    Chains: A, K
    Fragment: ALPHA CHAIN
    Organelle: CHLOROPLAST
    Organism Scientific: GRACILARIA CHILENSIS
    Organism Taxid: 2775
 
Molecule 2 - R-PHYCOERYTHRIN
    Chains: B, L
    Fragment: BETA CHAIN
    Organelle: CHLOROPLAST
    Organism Scientific: GRACILARIA CHILENSIS
    Organism Taxid: 2775
 
Molecule 3 - R-PHYCOERYTHRIN
    Chains: G, H
    Fragment: GAMMA CHAIN
    Organelle: CHLOROPLAST
    Organism Scientific: GRACILARIA CHILENSIS
    Organism Taxid: 2775

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABGHKL
Biological Unit 1 (1x): ABGHKL
Biological Unit 2 (3x): ABGHKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
1BLA1Ligand/IonBILIVERDINE IX ALPHA
2CYC7Ligand/IonPHYCOCYANOBILIN
3MEN2Mod. Amino AcidN-METHYL ASPARAGINE
4PUB2Ligand/IonPHYCOUROBILIN
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 14)
No.NameCountTypeFull Name
1BLA1Ligand/IonBILIVERDINE IX ALPHA
2CYC7Ligand/IonPHYCOCYANOBILIN
3MEN2Mod. Amino AcidN-METHYL ASPARAGINE
4PUB2Ligand/IonPHYCOUROBILIN
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (5, 42)
No.NameCountTypeFull Name
1BLA3Ligand/IonBILIVERDINE IX ALPHA
2CYC21Ligand/IonPHYCOCYANOBILIN
3MEN6Mod. Amino AcidN-METHYL ASPARAGINE
4PUB6Ligand/IonPHYCOUROBILIN
5SO46Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:68BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREGLY B:100 , GLU B:164BINDING SITE FOR RESIDUE SO4 B 202
03AC3SOFTWAREPHE A:60 , ALA A:72 , 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:372 , SER B:57 , ILE B:67 , TYR B:74 , THR B:75 , ASN B:76 , MET B:79BINDING SITE FOR RESIDUE BLA A 166
04AC4SOFTWARELEU A:44 , ASN A:47 , VAL A:51 , GLU A:54 , ARG A:137 , CYS A:139 , ARG A:142 , ASP A:143 , TYR A:152 , SER B:147 , GLN B:148 , PUB B:179BINDING SITE FOR RESIDUE CYC A 168
05AC5SOFTWARECYC A:168 , CYS B:50 , ASP B:54 , CYS B:61 , GLU B:62 , ARG B:129 , ILE B:133 , ALA B:137 , ALA B:140 , SER B:147 , GLN B:148 , ARG B:149BINDING SITE FOR RESIDUE PUB B 179
06AC6SOFTWAREMET B:59 , LEU B:66 , 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 , TYR B:117 , LEU B:120 , VAL B:122 , PRO B:123 , THR B:127BINDING SITE FOR RESIDUE CYC B 181
07AC7SOFTWARELEU A:24 , GLN A:28 , ASP B:33 , ASN B:35 , LYS B:36 , LEU B:38 , ASP B:39 , ILE B:142 , SER B:143 , ASN B:144 , VAL B:153 , ILE B:154 , GLU B:155 , GLY B:156 , CYS B:158 , ARG K:33 , GLN K:147BINDING SITE FOR RESIDUE CYC B 183
08AC8SOFTWAREPHE K:60 , ALA K:72 , LYS K:78 , LYS K:81 , CYS K:82 , ARG K:84 , ASP K:85 , HIS K:88 , TYR K:89 , TRP K:108 , TYR K:117 , LEU K:120 , LEU K:122 , ALA K:126 , TYR K:127 , HOH K:326 , HOH K:377 , ILE L:67 , TYR L:74 , THR L:75 , ASN L:76 , MET L:79BINDING SITE FOR RESIDUE CYC K 166
09AC9SOFTWARELEU K:44 , ASN K:47 , GLU K:54 , ARG K:137 , LEU K:138 , CYS K:139 , ARG K:142 , ASP K:143 , TYR K:152 , GLU L:155 , GLY L:156 , CYS L:158 , SER L:159 , CYC L:183BINDING SITE FOR RESIDUE CYC K 168
10BC1SOFTWARECYS L:50 , ASP L:54 , CYS L:61 , GLU L:62 , ARG L:129 , ILE L:133 , ALA L:136 , ALA L:137 , SER L:147 , GLN L:148 , HOH L:344BINDING SITE FOR RESIDUE PUB L 179
11BC2SOFTWAREPHE H:2 , MET L:59 , LEU L:66 , MEN L:72 , CYS L:73 , ARG L:77 , ARG L:78 , ALA L:81 , CYS L:82 , ARG L:84 , ASP L:85 , ILE L:88 , ARG L:108 , LEU L:113 , LEU L:120 , VAL L:122 , PRO L:123 , SER L:126 , THR L:127BINDING SITE FOR RESIDUE CYC L 181
12BC3SOFTWAREARG A:33 , GLN A:147 , HOH A:369 , LEU K:24 , GLN K:28 , CYC K:168 , ASN L:35 , LYS L:36 , LEU L:38 , ASP L:39 , ILE L:142 , SER L:143 , ASN L:144 , VAL L:153 , ILE L:154 , GLU L:155 , GLY L:156 , CYS L:158BINDING SITE FOR RESIDUE CYC L 183

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EYX)

(-) 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 PHEA_GRACH | Q7SIG0 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           PHEA_GRACH     1 MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGENQEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDRLCGPRDMSAQAGVEYSTALDYIINSLS 164
               SCOP domains d1eyxa_ A: Phycoerythrin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1eyxA00 A:1-164 Phycocyanins                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eyx A   1 MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGENQEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDRLCGPRDMSAQAGVEYSTALDYIINSLS 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 PHEB_GRACH | Q7SIF9 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
           PHEB_GRACH     1 MLDAFSRVISNADAKAAYVGGSDLQALRTFISDGNKRLDAVNYIVSNSSCIVSDAISGMICENPGLITPGGNCYTNRRMAACLRDGEIILRYISYALLAGDSSVLEDRCLNGLKETYIALGVPTNSTVRAVSIMKAAVGAFISNTASQRKGEVIEGDCSALAAEIASYCDRISAAVS 177
               SCOP domains d1eyxb_ B: Phycoerythrin beta subunit                                                                                                                                             SCOP domains
               CATH domains 1eyxB00 B:1-177 Phycocyanins                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eyx B   1 MLDAFSRVISNADAKAAYVGGSDLQALRTFISDGNKRLDAVNYIVSNSSCIVSDAISGMICENPGLITPGGnCYTNRRMAACLRDGEIILRYISYALLAGDSSVLEDRCLNGLKETYIALGVPTNSTVRAVSIMKAAVGAFISNTASQRKGEVIEGDCSALAAEIASYCDRISAAVS 177
                                    10        20        30        40        50        60        70 |      80        90       100       110       120       130       140       150       160       170       
                                                                                                  72-MEN                                                                                                     


Chain G from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author hhhhhh Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1eyx G   1 AAFRAA   6


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1eyx H   1 AFRAA   5


Chain K from PDB  Type:PROTEIN  Length:164
 aligned with PHEA_GRACH | Q7SIG0 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           PHEA_GRACH     1 MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGENQEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDRLCGPRDMSAQAGVEYSTALDYIINSLS 164
               SCOP domains d1eyxk_ K: Phycoerythrin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1eyxK00 K:1-164 Phycocyanins                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eyx K   1 MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGENQEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDRLCGPRDMSAQAGVEYSTALDYIINSLS 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain L from PDB  Type:PROTEIN  Length:177
 aligned with PHEB_GRACH | Q7SIF9 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
           PHEB_GRACH     1 MLDAFSRVISNADAKAAYVGGSDLQALRTFISDGNKRLDAVNYIVSNSSCIVSDAISGMICENPGLITPGGNCYTNRRMAACLRDGEIILRYISYALLAGDSSVLEDRCLNGLKETYIALGVPTNSTVRAVSIMKAAVGAFISNTASQRKGEVIEGDCSALAAEIASYCDRISAAVS 177
               SCOP domains d1eyxl_ L: Phycoerythrin beta subunit                                                                                                                                             SCOP domains
               CATH domains 1eyxL00 L:1-177 Phycocyanins                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eyx L   1 MLDAFSRVISNADAKAAYVGGSDLQALRTFISDGNKRLDAVNYIVSNSSCIVSDAISGMICENPGLITPGGnCYTNRRMAACLRDGEIILRYISYALLAGDSSVLEDRCLNGLKETYIALGVPTNSTVRAVSIMKAAVGAFISNTASQRKGEVIEGDCSALAAEIASYCDRISAAVS 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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EYX)

(-) Gene Ontology  (9, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,K   (PHEA_GRACH | Q7SIG0)
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,L   (PHEB_GRACH | Q7SIF9)
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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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PHEA_GRACH | Q7SIG0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PHEB_GRACH | Q7SIF9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1EYX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EYX)