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PDBsum entry 1luc

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Flavoprotein PDB id
1luc
Jmol
Contents
Protein chains
326 a.a. *
320 a.a. *
Ligands
EDO ×5
Metals
_MG ×3
Waters ×638
* Residue conservation analysis
PDB id:
1luc
Name: Flavoprotein
Title: Bacterial luciferase
Structure: Bacterial luciferase. Chain: a. Engineered: yes. Bacterial luciferase. Chain: b. Engineered: yes
Source: Vibrio harveyi. Organism_taxid: 669. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.182    
Authors: A.J.Fisher,I.Rayment
Key ref:
A.J.Fisher et al. (1996). The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions. J Biol Chem, 271, 21956-21968. PubMed id: 8703001 DOI: 10.1074/jbc.271.36.21956
Date:
10-May-96     Release date:   07-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07740  (LUXA_VIBHA) -  Alkanal monooxygenase alpha chain
Seq:
Struc:
355 a.a.
326 a.a.
Protein chain
Pfam   ArchSchema ?
P07739  (LUXB_VIBHA) -  Alkanal monooxygenase beta chain
Seq:
Struc:
324 a.a.
320 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.14.14.3  - Alkanal monooxygenase (FMN-linked).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RCHO + reduced FMN + O2 = RCOOH + FMN + H2O + light
RCHO
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ reduced FMN
+ O(2)
= RCOOH
+ FMN
+ H(2)O
+ light
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.271.36.21956 J Biol Chem 271:21956-21968 (1996)
PubMed id: 8703001  
 
 
The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.
A.J.Fisher, T.B.Thompson, J.B.Thoden, T.O.Baldwin, I.Rayment.
 
  ABSTRACT  
 
Bacterial luciferase is a flavin monooxygenase that catalyzes the oxidation of a long-chain aldehyde and releases energy in the form of visible light. A new crystal form of luciferase cloned from Vibrio harveyi has been grown under low-salt concentrations, which diffract x-rays beyond 1.5-A resolution. The x-ray structure of bacterial luciferase has been refined to a conventional R-factor of 18.2% for all recorded synchrotron data between 30.0 and 1.50-A resolution. Bacterial luciferase is an alpha-beta heterodimer, and the individual subunits fold into a single domain (beta/alpha)8 barrel. The high resolution structure reveals a non-prolyl cis peptide bond that forms between Ala74 and Ala75 in the alpha subunit near the putative active site. This cis peptide bond may have functional significance for creating a cavity at the active site. Bacterial luciferase employs reduced flavin as a substrate rather than a cofactor. The structure presented was determined in the absence of substrates. A comparison of the structural similarities between luciferase and a nonfluorescent flavoprotein, which is expressed in the lux operon of one genus of bioluminescent bacteria, suggests that the two proteins originated from a common ancestor. However, the flavin binding sites of the nonfluorescent protein are likely not representative of the flavin binding site on luciferase. The structure presented here will furnish a detailed molecular model for all bacterial luciferases.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Luciferase structure. Stereo ribbon representation of bacterial luciferase generated with the program MOLSCRIPT (72). The view is perpendicular to the pseudo 2-fold axis that lies horizontal in the plane of the page. The pseudo 2-fold axis relates the subunit shown in blue to the subunit in red. The eight core helices are labeled in the subunit.
Figure 3.
Fig. 3. Topology diagram. Cartoon showing the secondary structural elements of the two luciferase subunits (adapted from Ref. 16). -Strands and -helices are represented by arrows and cylinders, respectively. The ( / )[8] core is drawn flat along the middle with the loop insertions drawn above and below the core. 8 wraps around and hydrogen bonds to 1 to form the closed barrel. The numbers refer to the beginning and end of each secondary structural element.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1996, 271, 21956-21968) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21285948 B.El Yacoubi, I.Hatin, C.Deutsch, T.Kahveci, J.P.Rousset, D.Iwata-Reuyl, A.G Murzin, and V.de Crécy-Lagard (2011).
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification.
  EMBO J, 30, 882-893.  
20593108 M.Imani, S.Hosseinkhani, S.Ahmadian, and M.Nazari (2010).
Design and introduction of a disulfide bridge in firefly luciferase: increase of thermostability and decrease of pH sensitivity.
  Photochem Photobiol Sci, 9, 1167-1177.  
20520597 S.Boakes, A.N.Appleyard, J.Cortés, and M.J.Dawson (2010).
Organization of the biosynthetic genes encoding deoxyactagardine B (DAB), a new lantibiotic produced by Actinoplanes liguriae NCIMB41362.
  J Antibiot (Tokyo), 63, 351-358.  
19323825 M.Muto, R.E.Henry, and S.P.Mayfield (2009).
Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast.
  BMC Biotechnol, 9, 26.  
19710008 Z.T.Campbell, and T.O.Baldwin (2009).
Two lysine residues in the bacterial luciferase mobile loop stabilize reaction intermediates.
  J Biol Chem, 284, 32827-32834.  
17239244 S.Subbian, P.K.Mehta, S.L.Cirillo, and J.D.Cirillo (2007).
The Mycobacterium marinum mel2 locus displays similarity to bacterial bioluminescence systems and plays a role in defense against reactive oxygen and nitrogen species.
  BMC Microbiol, 7, 4.  
16807964 I.Müller, S.Weinig, H.Steinmetz, B.Kunze, S.Veluthoor, T.Mahmud, and R.Müller (2006).
A unique mechanism for methyl ester formation via an amide intermediate found in myxobacteria.
  Chembiochem, 7, 1197-1205.  
16997955 K.Abdurachim, and H.R.Ellis (2006).
Detection of protein-protein interactions in the alkanesulfonate monooxygenase system from Escherichia coli.
  J Bacteriol, 188, 8153-8159.  
15665092 L.W.Schultz, L.Liu, M.Cegielski, and J.W.Hastings (2005).
Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole.
  Proc Natl Acad Sci U S A, 102, 1378-1383.
PDB code: 1vpr
15726624 M.Babor, H.M.Greenblatt, M.Edelman, and V.Sobolev (2005).
Flexibility of metal binding sites in proteins on a database scale.
  Proteins, 59, 221-230.  
15937276 S.W.Aufhammer, E.Warkentin, U.Ermler, C.H.Hagemeier, R.K.Thauer, and S.Shima (2005).
Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family.
  Protein Sci, 14, 1840-1849.
PDB code: 1z69
12596267 T.Hamelryck (2003).
Efficient identification of side-chain patterns using a multidimensional index tree.
  Proteins, 51, 96.  
11900533 J.K.Inlow, and T.O.Baldwin (2002).
Mutational analysis of the subunit interface of Vibrio harveyi bacterial luciferase.
  Biochemistry, 41, 3906-3915.  
12146958 L.Y.Lin, T.Sulea, R.Szittner, C.Kor, E.O.Purisima, and E.A.Meighen (2002).
Implications of the reactive thiol and the proximal non-proline cis-peptide bond in the Structure and function of Vibrio harveyi luciferase.
  Biochemistry, 41, 9938-9945.  
11512142 I.E.Sukovataya, and N.A.Tyulkova (2001).
Kinetic analysis of bacterial bioluminescence in water-organic media.
  Luminescence, 16, 271-273.  
11468353 L.Y.Lin, T.Sulea, R.Szittner, V.Vassilyev, E.O.Purisima, and E.A.Meighen (2001).
Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data.
  Protein Sci, 10, 1563-1571.  
11683878 P.Chaiyen, C.Suadee, and P.Wilairat (2001).
A novel two-protein component flavoprotein hydroxylase.
  Eur J Biochem, 268, 5550-5561.  
11761334 S.C.Tu (2001).
Reduced flavin: donor and acceptor enzymes and mechanisms of channeling.
  Antioxid Redox Signal, 3, 881-897.  
10848974 J.Tyedmers, M.Kruse, M.Lerner, J.Demand, J.Höhfeld, J.Solsbacher, J.Volkmer, and R.Zimmermann (2000).
Assembly of heterodimeric luciferase after de novo synthesis of subunits in rabbit reticulocyte lysate involves hsc70 and hsp40 at a post-translational stage.
  Eur J Biochem, 267, 3575-3582.  
10587436 B.W.Noland, L.J.Dangott, and T.O.Baldwin (1999).
Folding, stability, and physical properties of the alpha subunit of bacterial luciferase.
  Biochemistry, 38, 16136-16145.  
10194361 H.Li, B.C.Ortego, K.I.Maillard, R.C.Willson, and S.C.Tu (1999).
Effects of mutations of the alpha His45 residue of Vibrio harveyi luciferase on the yield and reactivity of the flavin peroxide intermediate.
  Biochemistry, 38, 4409-4415.  
10490104 Q.Xu, D.Buckley, C.Guan, and H.C.Guo (1999).
Structural insights into the mechanism of intramolecular proteolysis.
  Cell, 98, 651-661.
PDB codes: 9gaa 9gac 9gaf
9772191 B.Lei, and S.C.Tu (1998).
Mechanism of reduced flavin transfer from Vibrio harveyi NADPH-FMN oxidoreductase to luciferase.
  Biochemistry, 37, 14623-14629.  
9665697 M.S.Hasson, A.Muscate, M.J.McLeish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, and D.Ringe (1998).
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
  Biochemistry, 37, 9918-9930.
PDB code: 1bfd
9790669 P.J.Focia, S.P.Craig, R.Nieves-Alicea, R.J.Fletterick, and A.E.Eakin (1998).
A 1.4 A crystal structure for the hypoxanthine phosphoribosyltransferase of Trypanosoma cruzi.
  Biochemistry, 37, 15066-15075.
PDB code: 1tc1
9891783 T.Wilson, and J.W.Hastings (1998).
Bioluminescence.
  Annu Rev Cell Dev Biol, 14, 197-230.  
9048575 A.C.Clark, S.W.Raso, J.F.Sinclair, M.M.Ziegler, A.F.Chaffotte, and T.O.Baldwin (1997).
Kinetic mechanism of luciferase subunit folding and assembly.
  Biochemistry, 36, 1891-1899.  
  9007973 J.B.Thoden, H.M.Holden, A.J.Fisher, J.F.Sinclair, G.Wesenberg, T.O.Baldwin, and I.Rayment (1997).
Structure of the beta 2 homodimer of bacterial luciferase from Vibrio harveyi: X-ray analysis of a kinetic protein folding trap.
  Protein Sci, 6, 13-23.
PDB code: 1bsl
9020763 J.J.Tanner, M.D.Miller, K.S.Wilson, S.C.Tu, and K.L.Krause (1997).
Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding.
  Biochemistry, 36, 665-672.
PDB code: 1xkj
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.