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(-) Description

Title :  CRYSTAL STRUCTURE OF A LUCIFERASE DOMAIN FROM THE DINOFLAGELLATE LINGULODINIUM POLYEDRUM
 
Authors :  L. W. Schultz, L. Liu, M. Cegielski, J. W. Hastings
Date :  15 Nov 04  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Fatty Acid Binding Protein, Lipocalin, Luciferase, Ph Regulation, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Schultz, L. Liu, M. Cegielski, J. W. Hastings
Crystal Structure Of A Ph-Regulated Luciferase Catalyzing The Bioluminescent Oxidation Of An Open Tetrapyrrole
Proc. Natl. Acad. Sci. Usa V. 102 1378 2005
PubMed-ID: 15665092  |  Reference-DOI: 10.1073/PNAS.0409335102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUCIFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 866-1241
    Organism Scientific: LINGULODINIUM POLYEDRUM
    Organism Taxid: 160621

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VPR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:1213 -Pro A:1214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VPR)

(-) 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:351
 aligned with LUCIF_LINPO | O77206 from UniProtKB/Swiss-Prot  Length:1241

    Alignment length:351
                                   877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217 
         LUCIF_LINPO    868 EKGFEAGDNKLGGALNAKHVEKYGDNFKNGMHKPEFHEDGLHKPMEVGGKKFESGFHYLLECHELGGKNASGGYGGPLCEDPYGSEVQAMTEKLLKEADSDRTLCFNNFQDPCPQLTKEQVAMCKGFDYGDKTLKLPCGPLPWPAGLPEPGYVPKTNPLHGRWITVSGGQAAFIKEAIKSGMLGAAEANKIVADTDHHQTGGMYLRINQFGDVCTVDASVAKFARAKRTWKSGHYFYEPLVSGGNLLGVWVLPEEYRKIGFFWEMESGRCFRIERRAFPVGPYTFMRQATEVGGKISFVFYVKVSNDPESDPIPLQSRDYTALAGRDNAPTNLGKPYPTLAKDLDYPKKRD 1218
               SCOP domains d1vpra1 A:868-1218 Dinoflagellate luciferase                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhh.ee..ee............eee..eee.hhhhhhhhhhh...................hhhhhhhhhhhhhhhh....hhhhhhh......hhhhhhhhh...................................eeeeeee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeeee..eeeee.........eeeee...eeeee.....eeeeeee.....eeeeeeee.....eeeeeeeeeee..eeeeeeeeee..eeeeeeeeeee............hhhhhh............................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vpr A  868 EKGFEAGDNKLGGALNAKHVEKYGDNFKNGmHKPEFHEDGLHKPmEVGGKKFESGFHYLLECHELGGKNASGGYGGPLCEDPYGSEVQAmTEKLLKEADSDRTLCFNNFQDPCPQLTKEQVAmCKGFDYGDKTLKLPCGPLPWPAGLPEPGYVPKTNPLHGRWITVSGGQAAFIKEAIKSGMLGAAEANKIVADTDHHQTGGmYLRINQFGDVCTVDASVAKFARAKRTWKSGHYFYEPLVSGGNLLGVWVLPEEYRKIGFFWEmESGRCFRIERRAFPVGPYTFmRQATEVGGKISFVFYVKVSNDPESDPIPLQSRDYTALAGRDNAPTNLGKPYPTLAKDLDYPKKRD 1218
                                   877       887       897|      907    |  917       927       937       947       957       967       977       987  |    997      1007      1017      1027      1037      1047      1057      1067  |   1077      1087      1097      1107      1117      1127    | 1137      1147     |1157      1167      1177      1187      1197      1207      1217 
                                                        898-MSE       912-MSE                                      957-MSE                          990-MSE                                                                        1070-MSE                                                      1132-MSE             1153-MSE
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VPR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LUCIF_LINPO | O77206)
molecular function
    GO:0045289    luciferin monooxygenase activity    Catalysis of the generalized reaction: luciferin + O2 = oxidized luciferin + CO2 + light. There may be additional substrates and reactants involved in the reaction. The reaction results in light emission as luciferin returns to the ground state after enzymatic oxidation.
    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:0016703    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases)    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and one oxygen atom is incorporated into a donor.
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    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.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.

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    Tyr A:1213 - Pro A:1214   [ RasMol ]  
 

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