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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION
 
Authors :  A. J. Fisher, I. Rayment
Date :  20 Mar 95  (Deposition) - 01 Apr 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Monooxygenase, Luminescence (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Fisher, F. M. Raushel, T. O. Baldwin, I. Rayment
Three-Dimensional Structure Of Bacterial Luciferase From Vibrio Harveyi At 2. 4 A Resolution.
Biochemistry V. 34 6581 1995
PubMed-ID: 7756289  |  Reference-DOI: 10.1021/BI00020A002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIAL LUCIFERASE
    ChainsA, C
    EC Number1.14.14.3
    Organism ScientificVIBRIO HARVEYI
    Organism Taxid669
    Other DetailsAPO (NO FMN)
 
Molecule 2 - BACTERIAL LUCIFERASE
    ChainsB, D
    EC Number1.14.14.3
    Organism ScientificVIBRIO HARVEYI
    Organism Taxid669
    Other DetailsAPO (NO FMN)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:107 , VAL A:173 , GLU A:175 , SER A:176 , THR A:179 , HOH A:2010BINDING SITE FOR RESIDUE PO4 A 356

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:159 -Pro A:160
2Asn B:159 -Pro B:160
3Asn C:159 -Pro C:160
4Asn D:159 -Pro D:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_LUCIFERASEPS00494 Bacterial luciferase subunits signature.LUXB_VIBHA187-212
 
  2B:187-212
D:187-212
LUXA_VIBHA187-212
 
  2A:187-212
C:187-212
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_LUCIFERASEPS00494 Bacterial luciferase subunits signature.LUXB_VIBHA187-212
 
  1B:187-212
-
LUXA_VIBHA187-212
 
  1A:187-212
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_LUCIFERASEPS00494 Bacterial luciferase subunits signature.LUXB_VIBHA187-212
 
  1-
D:187-212
LUXA_VIBHA187-212
 
  1-
C:187-212

(-) Exons   (0, 0)

(no "Exon" information available for 1BRL)

(-) 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:340
 aligned with LUXA_VIBHA | P07740 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:355
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350     
           LUXA_VIBHA     1 MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEHHFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYDFNKGQWRDFVLKGHKDTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEEEIIASMKLFQSDVMPYLKEKQ 355
               SCOP domains d1brla_ A: Bacterial luciferase alpha chain, LuxA                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1brlA00 A:1-355 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhee...........ee............eeee..hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhh.........eeeee.ee..hhhhhhhhhhhhhhhhhhhhhhh..............---------------.......hhhhhh.eehhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_LUCIFERASE      ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brl A   1 MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEHHFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYD---------------DTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEEEIIASMKLFQSDVMPYLKEKQ 355
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|        -      |290       300       310       320       330       340       350     
                                                                                                                                                                                                                                                                                                        271             287                                                                    

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with LUXB_VIBHA | P07739 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
           LUXB_VIBHA     1 MKFGLFFLNFMNSKRSSDQVIEEMLDTAHYVDQLKFDTLAVYENHFSNNGVVGAPLTVAGFLLGMTKNAKVASLNHVITTHHPVRVAEEACLLDQMSEGRFAFGFSDCEKSADMRFFNRPTDSQFQLFSECHKIINDAFTTGYCHPNNDFYSFPKISVNPHAFTEGGPAQFVNATSKEVVEWAAKLGLPLVFRWDDSNAQRKEYAGLYHEVAQAHGVDVSQVRHKLTLLVNQNVDGEAARAEARVYLEEFVRESYSNTDFEQKMGELLSENAIGTYEESTQAARVAIECCGAADLLMSFESMEDKAQQRAVIDVVNANI 319
               SCOP domains d1brlb_ B: Bacterial luciferase beta chain, LuxB                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1brlB00 B:1-319 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhee...........ee..................hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_LUCIFERASE      ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brl B   1 MKFGLFFLNFMNSKRSSDQVIEEMLDTAHYVDQLKFDTLAVYENHFSNNGVVGAPLTVAGFLLGMTKNAKVASLNHVITTHHPVRVAEEACLLDQMSEGRFAFGFSDCEKSADMRFFNRPTDSQFQLFSECHKIINDAFTTGYCHPNNDFYSFPKISVNPHAFTEGGPAQFVNATSKEVVEWAAKLGLPLVFRWDDSNAQRKEYAGLYHEVAQAHGVDVSQVRHKLTLLVNQNVDGEAARAEARVYLEEFVRESYSNTDFEQKMGELLSENAIGTYEESTQAARVAIECCGAADLLMSFESMEDKAQQRAVIDVVNANI 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         

Chain C from PDB  Type:PROTEIN  Length:340
 aligned with LUXA_VIBHA | P07740 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:355
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350     
           LUXA_VIBHA     1 MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEHHFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYDFNKGQWRDFVLKGHKDTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEEEIIASMKLFQSDVMPYLKEKQ 355
               SCOP domains d1brlc_ C: Bacterial luciferase alpha chain, LuxA                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1brlC00 C:1-355 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhee...........ee............eeee..hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhh.........eeeee.ee..hhhhhhhhhhhhhhhhhhhhhhh..............---------------.......hhhhhh.eehhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_LUCIFERASE      ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brl C   1 MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEHHFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYD---------------DTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEEEIIASMKLFQSDVMPYLKEKQ 355
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|        -      |290       300       310       320       330       340       350     
                                                                                                                                                                                                                                                                                                        271             287                                                                    

Chain D from PDB  Type:PROTEIN  Length:319
 aligned with LUXB_VIBHA | P07739 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
           LUXB_VIBHA     1 MKFGLFFLNFMNSKRSSDQVIEEMLDTAHYVDQLKFDTLAVYENHFSNNGVVGAPLTVAGFLLGMTKNAKVASLNHVITTHHPVRVAEEACLLDQMSEGRFAFGFSDCEKSADMRFFNRPTDSQFQLFSECHKIINDAFTTGYCHPNNDFYSFPKISVNPHAFTEGGPAQFVNATSKEVVEWAAKLGLPLVFRWDDSNAQRKEYAGLYHEVAQAHGVDVSQVRHKLTLLVNQNVDGEAARAEARVYLEEFVRESYSNTDFEQKMGELLSENAIGTYEESTQAARVAIECCGAADLLMSFESMEDKAQQRAVIDVVNANI 319
               SCOP domains d1brld_ D: Bacterial luciferase beta chain, LuxB                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1brlD00 D:1-319 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhee...........ee..................hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_LUCIFERASE      ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brl D   1 MKFGLFFLNFMNSKRSSDQVIEEMLDTAHYVDQLKFDTLAVYENHFSNNGVVGAPLTVAGFLLGMTKNAKVASLNHVITTHHPVRVAEEACLLDQMSEGRFAFGFSDCEKSADMRFFNRPTDSQFQLFSECHKIINDAFTTGYCHPNNDFYSFPKISVNPHAFTEGGPAQFVNATSKEVVEWAAKLGLPLVFRWDDSNAQRKEYAGLYHEVAQAHGVDVSQVRHKLTLLVNQNVDGEAARAEARVYLEEFVRESYSNTDFEQKMGELLSENAIGTYEESTQAARVAIECCGAADLLMSFESMEDKAQQRAVIDVVNANI 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (LUXA_VIBHA | P07740)
molecular function
    GO:0047646    alkanal monooxygenase (FMN-linked) activity    Catalysis of the reaction: R-CHO + reduced FMN + O2 = R-COOH + FMN + H2O + light.
    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.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or 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.

Chain B,D   (LUXB_VIBHA | P07739)
molecular function
    GO:0047646    alkanal monooxygenase (FMN-linked) activity    Catalysis of the reaction: R-CHO + reduced FMN + O2 = R-COOH + FMN + H2O + light.
    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.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LUXA_VIBHA | P077401luc 3fgc
        LUXB_VIBHA | P077391bsl 1luc 1xkj 3fgc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BRL)