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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBSTRATE-FREE FORM OF PCYA
 
Authors :  Y. Hagiwara, M. Sugishima, Y. Takahashi, K. Fukuyama
Date :  10 Apr 06  (Deposition) - 25 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta-Alpha Sandwich, Substrate Free Form, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hagiwara, M. Sugishima, Y. Takahashi, K. Fukuyama
Induced-Fitting And Electrostatic Potential Change Of Pcya Upon Substrate Binding Demonstrated By The Crystal Structur Of The Substrate-Free Form
Febs Lett. V. 580 3823 2006
PubMed-ID: 16782089  |  Reference-DOI: 10.1016/J.FEBSLET.2006.05.075

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 1.3.7.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:221BINDING SITE FOR RESIDUE CL A 249

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DKE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DKE)

(-) Sequences/Alignments

Asymmetric/Biological 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:241
 aligned with PCYA_SYNY3 | Q55891 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 
           PCYA_SYNY3     5 DLSLTNSSLMPTLNPMIQQLALAIAASWQSLPLKPYQLPEDLGYVEGRLEGEKLVIENRCYQTPQFRKMHLELAKVGKGLDILHCVMFPEPLYGLPLFGCDIVAGPGGVSAAIADLSPTQSDRQLPAAYQKSLAELGQPEFEQQRELPPWGEIFSEYCLFIRPSNVTEEERFVQRVVDFLQIHCHQSIVAEPLSEAQTLEHRQGQIHYCQQQQKNDKTRRVLEKAFGEAWAERYMSQVLFD 245
               SCOP domains d2dkea_ A: Ferredoxin-dependent bilin reductase                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhh...ee...hhhh.eeeeee..eeeeeeeeeeee..eeeeeeeeeee....eeeeeeeee.hhhh..eeeeeeeee..eeeeeeeeee........hhhhhhhhhhh.............hhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dke A   5 DLSLTNSSLMPTLNPMIQQLALAIAASWQSLPLKPYQLPEDLGYVEGRLEGEKLVIENRCYQTPQFRKMHLELAKVGKGLDILHCVMFPEPLYGLPLFGCDIVAGPGGVSAAIADLSPTQSDRQLPAAYQKSLAELGQPEFEQQRELPPWGEIFSEYCLFIRPSNVTEEERFVQRVVDFLQIHCHQSIVAEPLSEAQTLEHRQGQIHYCQQQQKNDKTRRVLEKAFGEAWAERYMSQVLFD 245
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DKE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DKE)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PCYA_SYNY3 | Q55891)
molecular function
    GO:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016636    oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces an iron-sulfur protein.
    GO:0050620    phycocyanobilin:ferredoxin oxidoreductase activity    Catalysis of the reaction: (3Z)-phycocyanobilin + oxidized ferredoxin = biliverdin IXa + reduced ferredoxin.
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:0010024    phytochromobilin biosynthetic process    The chemical reactions and pathways resulting in the formation of phytochromobilin, which involves the oxidative cleavage of heme by a heme oxygenase(HO) to form biliverdin IX alpha.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCYA_SYNY3 | Q55891: 2d1e 3ajg 3ajh 3f0l 3f0m 3i8u 3i94 3i95 3nb8 3nb9 4eoc 4eod 4eoe 4qcd 5b4h 5b4i 5b4j

(-) Related Entries Specified in the PDB File

2d1e THE SAME PROTEIN COMPLEXED WITH BILIVERDIN IXALPHA