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(-) Description

Title :  CRYSTAL STRUCTURES OF THE LUCIFERASE AND GREEN FLUORESCENT PROTEIN FROM RENILLA RENIFORMIS
 
Authors :  A. M. Loening, T. D. Fenn, S. S. Gambhir
Date :  06 May 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta-Hydrolase, Luciferase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. M. Loening, T. D. Fenn, S. S. Gambhir
Crystal Structures Of The Luciferase And Green Fluorescent Protein From Renilla Reniformis.
J. Mol. Biol. V. 374 1017 2007
PubMed-ID: 17980388  |  Reference-DOI: 10.1016/J.JMB.2007.09.078

(-) Compounds

Molecule 1 - RENILLA-LUCIFERIN 2-MONOOXYGENASE
    ChainsA, B
    EC Number1.13.12.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBAD
    Expression System StrainLMG194
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRLUC
    MutationYES
    Organism ScientificRENILLA RENIFORMIS
    Organism Taxid6136
    SynonymRENILLA-TYPE LUCIFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CEI2Ligand/IonN-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CEI1Ligand/IonN-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CEI1Ligand/IonN-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:156 , ASP A:162 , MET A:174 , PHE A:180 , HIS A:285 , HOH A:655BINDING SITE FOR RESIDUE CEI A 501
2AC2SOFTWARETRP B:156 , ASP B:162 , MET B:174 , PHE B:180 , PHE B:261 , HIS B:285 , HOH B:680 , HOH B:698BINDING SITE FOR RESIDUE CEI B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:258 -Pro A:259
2Asp B:258 -Pro B:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PSJ)

(-) 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:306
 aligned with LUCI_RENRE | P27652 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:308
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
           LUCI_RENRE     3 SKVYDPEQRKRMITGPQWWARCKQMNVLDSFINYYDSEKHAENAVIFLHGNAASSYLWRHVVPHIEPVARCIIPDLIGMGKSGKSGNGSYRLLDHYKYLTAWFELLNLPKKIIFVGHDWGACLAFHYSYEHQDKIKAIVHAESVVDVIESWDEWPDIEEDIALIKSEEGEKMVLENNFFVETMLPSKIMRKLEPEEFAAYLEPFKEKGEVRRPTLSWPREIPLVKGGKPDVVQIVRNYNAYLRASDDLPKMFIESDPGFFSNAIVEGAKKFPNTEFVKVKGLHFSQEDAPDEMGKYIKSFVERVLKNE 310
               SCOP domains d2psja_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2psjA00 A:3-310  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhh.eeeee..eeeeeee.......eeeee.....hhhhhh.hhhhh....eeeee................hhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhh...eeeeeeeee.......--...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2psj A   3 SKVYDPEQRKRMITGPQWWARCKQMNVLDSFINYYDSEKHAENAVIFLHGNATSSYLWRHVVPHIEPVARCIIPDLIGMGKSGKSGNGSYRLLDHYKYLTAWFELLNLPKKIIFVGHDWGAALAFHYAYEHQDRIKAIVHMESVVDVIES--EWPDIEEDIALIKSEEGEKMVLENNFFVETVLPSKIMRKLEPEEFAAYLEPFKEKGEVRRPTLSWPREIPLVKGGKPDVVQIVRNYNAYLRASDDLPKLFIESDPGFFSNAIVEGAKKFPNTEFVKVKGLHFLQEDAPDEMGKYIKSFVERVLKNE 310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  |    162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
                                                                                                                                                                               152  |                                                                                                                                                           
                                                                                                                                                                                  155                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with LUCI_RENRE | P27652 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:308
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
           LUCI_RENRE     3 SKVYDPEQRKRMITGPQWWARCKQMNVLDSFINYYDSEKHAENAVIFLHGNAASSYLWRHVVPHIEPVARCIIPDLIGMGKSGKSGNGSYRLLDHYKYLTAWFELLNLPKKIIFVGHDWGACLAFHYSYEHQDKIKAIVHAESVVDVIESWDEWPDIEEDIALIKSEEGEKMVLENNFFVETMLPSKIMRKLEPEEFAAYLEPFKEKGEVRRPTLSWPREIPLVKGGKPDVVQIVRNYNAYLRASDDLPKMFIESDPGFFSNAIVEGAKKFPNTEFVKVKGLHFSQEDAPDEMGKYIKSFVERVLKNE 310
               SCOP domains d2psjb_ B: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2psjB00 B:3-310  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) --------------------------------------------------------------------Abhydrolase_1-2psjB01 B:71-301                                                                                                                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------Abhydrolase_1-2psjB02 B:71-301                                                                                                                                                                                                         --------- Pfam domains (2)
         Sec.struct. author .......hhhhh.hhhhhhhh.eeeee..eeeeeee.......eeeee.....hhhhhh.hhhhhh...eeeee................hhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhh...eeeeeeeee.......--...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh......eeeeeeee...hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2psj B   3 SKVYDPEQRKRMITGPQWWARCKQMNVLDSFINYYDSEKHAENAVIFLHGNATSSYLWRHVVPHIEPVARCIIPDLIGMGKSGKSGNGSYRLLDHYKYLTAWFELLNLPKKIIFVGHDWGAALAFHYAYEHQDRIKAIVHMESVVDVIES--EWPDIEEDIALIKSEEGEKMVLENNFFVETVLPSKIMRKLEPEEFAAYLEPFKEKGEVRRPTLSWPREIPLVKGGKPDVVQIVRNYNAYLRASDDLPKLFIESDPGFFSNAIVEGAKKFPNTEFVKVKGLHFLQEDAPDEMGKYIKSFVERVLKNE 310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  |    162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
                                                                                                                                                                               152  |                                                                                                                                                           
                                                                                                                                                                                  155                                                                                                                                                           

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LUCI_RENRE | P27652)
molecular function
    GO:0050248    Renilla-luciferin 2-monooxygenase activity    Catalysis of the reaction: Renilla luciferin + O2 = oxidized Renilla luciferin + CO2 + light.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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.
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.

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 Related Entries

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        LUCI_RENRE | P276522psd 2pse 2psf 2psh

(-) Related Entries Specified in the PDB File

2psd 2pse 2psf 2psh 2psl