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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED D105N SYNECHOCYSTIS SP. PCYA
 
Authors :  A. C. Kohler, D. D. Gae
Date :  25 Oct 08  (Deposition) - 13 Oct 09  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta-Alpha Sandwich, Radical Chemistry, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Kohler, D. D. Gae, M. A. Richley, S. Stoll, A. Gunn, S. Lim, S. S. Martin, T. I. Doukov, R. D. Britt, J. B. Ames, J. C. Lagarias, A. J. Fisher
Structural Basis For Hydration Dynamics In Radical Stabilization Of Bilin Reductase Mutants.
Biochemistry V. 49 6206 2010
PubMed-ID: 20557110  |  Reference-DOI: 10.1021/BI100728Q

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 1.3.7.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCYA, SLR0116
    Mutation: YES
    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  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1BLA1Ligand/IonBILIVERDINE IX ALPHA
2EDO11Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:20 , GLU A:173 , GLU A:174 , HOH A:1217 , HOH A:1239BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWARETYR A:40 , GLN A:41 , GLN A:66BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWAREPRO A:43 , GLU A:44 , TRP A:234 , ARG A:237 , HOH A:1029 , HOH A:1045BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREPRO A:122 , THR A:123 , GLN A:124 , ARG A:127 , GLY A:208 , EDO A:405 , HOH A:1081 , HOH A:1090 , HOH A:1107 , HOH A:1204BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREHIS A:211 , EDO A:404 , HOH A:1079 , HOH A:1195 , HOH A:1327BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREGLN A:124 , LEU A:197 , GLN A:201 , HIS A:205 , EDO A:412 , HOH A:1212 , HOH A:1214BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWARETHR A:171 , ARG A:175 , HOH A:1074BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREGLU A:232 , ALA A:233 , GLU A:236 , HOH A:1027 , HOH A:1077 , HOH A:1180BINDING SITE FOR RESIDUE EDO A 409
09AC9SOFTWAREALA A:132 , TYR A:133 , GLN A:190 , HOH A:1117 , HOH A:1309BINDING SITE FOR RESIDUE EDO A 410
10BC1SOFTWAREARG A:63 , CYS A:64 , TYR A:65 , HOH A:1082 , HOH A:1262 , HOH A:1374BINDING SITE FOR RESIDUE EDO A 411
11BC2SOFTWAREGLN A:124 , PRO A:130 , ALA A:131 , EDO A:406 , HOH A:1117 , HOH A:1149BINDING SITE FOR RESIDUE EDO A 412
12BC3SOFTWARESER A:34 , GLU A:76 , ILE A:86 , HIS A:88 , VAL A:90 , GLY A:103 , ASN A:105 , VAL A:107 , SER A:114 , ALA A:115 , ILE A:117 , ARG A:149 , PHE A:158 , PHE A:164 , ASN A:219 , LYS A:221 , THR A:222 , PHE A:244 , HOH A:1042 , HOH A:1067 , HOH A:1094 , HOH A:1104 , HOH A:1146 , HOH A:1171 , HOH A:1400BINDING SITE FOR RESIDUE BLA A 249

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F0L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F0L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F0L)

(-) Exons   (0, 0)

(no "Exon" information available for 3F0L)

(-) 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:243
 aligned with PCYA_SYNY3 | Q55891 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   
           PCYA_SYNY3     6 LSLTNSSLMPTLNPMIQQLALAIAASWQSLPLKPYQLPEDLGYVEGRLEGEKLVIENRCYQTPQFRKMHLELAKVGKGLDILHCVMFPEPLYGLPLFGCDIVAGPGGVSAAIADLSPTQSDRQLPAAYQKSLAELGQPEFEQQRELPPWGEIFSEYCLFIRPSNVTEEERFVQRVVDFLQIHCHQSIVAEPLSEAQTLEHRQGQIHYCQQQQKNDKTRRVLEKAFGEAWAERYMSQVLFDVIQ 248
               SCOP domains d3f0la_ A: Ferredoxin-dependent bilin reductase                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhh....ee..hhhhh..eee......eeeeeeeee...eeeeeeeeeee...eeeeeeeeee.hhhh..eeeeeeeee..eeeeeeeeee........hhhhhhhhhh............hhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0l A   6 LSLTNSSLMPTLNPMIQQLALAIAASWQSLPLKPYQLPEDLGYVEGRLEGEKLVIENRCYQTPQFRKMHLELAKVGKGLDILHCVMFPEPLYGLPLFGCNIVAGPGGVSAAIADLSPTQSDRQLPAAYQKSLAELGQPEFEQQRELPPWGEIFSEYCLFIRPSNVTEEERFVQRVVDFLQIHCHQSIVAEPLSEAQTLEHRQGQIHYCQQQQKNDKTRRVLEKAFGEAWAERYMSQVLFDVIQ 248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
   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 3F0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F0L)

(-) 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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  PCYA_SYNY3 | Q55891
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3f0j CRYSTAL STRUCTURE OF OXIDIZED H88Q SYNECHOCYSTIS SP. PCYA
3f0k CRYSTAL STRUCTURE OF RADICAL H88Q SYNECHOCYSTIS SP. PCYA
3f0m CRYSTAL STRUCTURE OF RADICAL D105N SYNECHOCYSTIS SP. PCYA