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(-) Description

Title :  STRUCTURE OF PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN THE SUBSTRATE FREE FORM
 
Authors :  T. Dammeyer, E. Hofmann, N. Frankenberg-Dinkel
Date :  25 Sep 07  (Deposition) - 05 Aug 08  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyanophages, Biliverdin Ixa, Oxidoreductase, Phycobilin Reductase, Phycobilin Synthesis, Prochlorococcus, Phycoerythrobilin, Biliverdin Reductase, Ferredoxin Dependent (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Dammeyer, E. Hofmann, N. Frankenberg-Dinkel
Phycoerythrobilin Synthase (Pebs) Of A Marine Virus: Crysta Structures Of The Biliverdin Complex And The Substrate-Free Form.
J. Biol. Chem. V. 283 27547 2008
PubMed-ID: 18662988  |  Reference-DOI: 10.1074/JBC.M803765200

(-) Compounds

Molecule 1 - CYANOBACTERIAL PHYCOERYTHROBILIN
    Chains: A
    EC Number: 1.3.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PROCHLOROCOCCUS PHAGE P-SSM2
    Organism Taxid: 268746
    Synonym: PHYCOBILIN REDUCTASE, CYANOPHAGE PHYCOERYTHROBILIN SYNTHASE PEBS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:113 , PHE A:143 , TYR A:158 , LEU A:168 , ASP A:169 , LYS A:172 , HOH A:2140 , HOH A:2162 , HOH A:2223 , HOH A:2224BINDING SITE FOR RESIDUE GOL A1234
2AC2SOFTWAREILE A:86 , ASN A:88 , ASP A:105 , PHE A:224BINDING SITE FOR RESIDUE GOL A1235
3AC3SOFTWAREGLY A:103 , MSE A:104 , GLN A:121 , MSE A:202 , HOH A:2225BINDING SITE FOR RESIDUE GOL A1236

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VCL)

(-) 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:205
 aligned with PEBS_BPPRM | Q58MU6 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:212
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
           PEBS_BPPRM    22 TIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Fe_bilin_red-2vclA01 A:25-2     31                                                                                                                                                                             -- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeeeeeeeee..-----..eeeeeeeeee..eeeeeeeeeee..eeeeeeeeee.......eeeeeeeeee..eeeeeeeee.................................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh--.hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vcl A  22 TIWQNYIDALFETFPQLEISEVWAKWDGGN-----GDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGmDLmKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEmGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEmIDNNKPVGEDTTVYSDFDTYmTEL--VRGYmKNKFGEGRSEAFVNDFLFSYK 233
                                    31        41        51     |  61        71        81        91       101  |  | 111       121       131       141    |  151       161       171       181       191       201|  |  |211|      221       231  
                                                        51    57                                            104-MSE                                   146-MSE                            181-MSE              202-MSE |   |                     
                                                                                                               107-MSE                                                                                           205  |   |                     
                                                                                                                                                                                                                    208   |                     
                                                                                                                                                                                                                        212-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2VCL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Fe_bilin_red] (8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PEBS_BPPRM | Q58MU6)
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.
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
        PEBS_BPPRM | Q58MU6: 2vck 2vgr 2x9i 2x9j

(-) Related Entries Specified in the PDB File

2vck STRUCTURE OF THE PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATE BILIVERDIN IXA
2vgr STRUCTURE OF THE WT-PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATE BILIVERDIN IXA