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PDBsum entry 1ba3

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protein ligands links
Oxidoreductase PDB id
1ba3
Jmol
Contents
Protein chain
540 a.a. *
Ligands
MBR ×2
Waters ×353
* Residue conservation analysis
PDB id:
1ba3
Name: Oxidoreductase
Title: Firefly luciferase in complex with bromoform
Structure: Luciferase. Chain: a. Engineered: yes
Source: Photinus pyralis. Common eastern firefly. Organism_taxid: 7054. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.20Å     R-factor:   0.197     R-free:   0.239
Authors: N.P.Franks,A.Jenkins,E.Conti,W.R.Lieb,P.Brick
Key ref: N.P.Franks et al. (1998). Structural basis for the inhibition of firefly luciferase by a general anesthetic. Biophys J, 75, 2205-2211. PubMed id: 9788915
Date:
21-Apr-98     Release date:   11-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08659  (LUCI_PHOPY) -  Luciferin 4-monooxygenase
Seq:
Struc:
 
Seq:
Struc:
550 a.a.
540 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.12.7  - Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Photinus-luciferin 4-monooxygenase (ATP-hydrolysing)
      Reaction: Photinus luciferin + O2 + ATP = oxidized Photinus luciferin + CO2 + AMP + diphosphate + light
Photinus luciferin
+ O(2)
+ ATP
= oxidized Photinus luciferin
+ CO(2)
+ AMP
+ diphosphate
+ light
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     peroxisome   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
Biophys J 75:2205-2211 (1998)
PubMed id: 9788915  
 
 
Structural basis for the inhibition of firefly luciferase by a general anesthetic.
N.P.Franks, A.Jenkins, E.Conti, W.R.Lieb, P.Brick.
 
  ABSTRACT  
 
The firefly luciferase enzyme from Photinus pyralis is probably the best-characterized model system for studying anesthetic-protein interactions. It binds a diverse range of general anesthetics over a large potency range, displays a sensitivity to anesthetics that is very similar to that found in animals, and has an anesthetic sensitivity that can be modulated by one of its substrates (ATP). In this paper we describe the properties of bromoform acting as a general anesthetic (in Rana temporaria tadpoles) and as an inhibitor of the firefly luciferase enzyme at high and low ATP concentrations. In addition, we describe the crystal structure of the low-ATP form of the luciferase enzyme in the presence of bromoform at 2.2-A resolution. These results provide a structural basis for understanding the anesthetic inhibition of the enzyme, as well as an explanation for the ATP modulation of its anesthetic sensitivity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21334330 M.J.Koetsier, P.A.Jekel, H.J.Wijma, R.A.Bovenberg, and D.B.Janssen (2011).
Aminoacyl-coenzyme A synthesis catalyzed by a CoA ligase from Penicillium chrysogenum.
  FEBS Lett, 585, 893-898.  
20505891 A.Lesarri, A.Vega-Toribio, R.D.Suenram, D.J.Brugh, and J.U.Grabow (2010).
The conformational landscape of the volatile anesthetic sevoflurane.
  Phys Chem Chem Phys, 12, 9624-9631.  
20660787 G.Brannigan, D.N.LeBard, J.Hénin, R.G.Eckenhoff, and M.L.Klein (2010).
Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain.
  Proc Natl Acad Sci U S A, 107, 14122-14127.  
19923209 T.V.Lee, L.J.Johnson, R.D.Johnson, A.Koulman, G.A.Lane, J.S.Lott, and V.L.Arcus (2010).
Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.
  J Biol Chem, 285, 2415-2427.
PDB code: 3ite
19559587 A.Taneoka, A.Sakaguchi-Mikami, T.Yamazaki, W.Tsugawa, and K.Sode (2009).
The construction of a glucose-sensing luciferase.
  Biosens Bioelectron, 25, 76-81.  
19332643 H.Zhang, N.S.Astrof, J.H.Liu, J.H.Wang, and M.Shimaoka (2009).
Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems.
  FASEB J, 23, 2735-2740.
PDB codes: 3f74 3f78
19605349 L.S.Vedula, G.Brannigan, N.J.Economou, J.Xi, M.A.Hall, R.Liu, M.J.Rossi, W.P.Dailey, K.C.Grasty, M.L.Klein, R.G.Eckenhoff, and P.J.Loll (2009).
A unitary anesthetic binding site at high resolution.
  J Biol Chem, 284, 24176-24184.
PDB codes: 3f32 3f33 3f34 3f35 3f36 3f37 3f38 3f39
19697903 L.T.Liu, D.Willenbring, Y.Xu, and P.Tang (2009).
General anesthetic binding to neuronal alpha4beta2 nicotinic acetylcholine receptor and its effects on global dynamics.
  J Phys Chem B, 113, 12581-12589.  
18821786 C.G.Canlas, T.Cui, L.Li, Y.Xu, and P.Tang (2008).
Anesthetic modulation of protein dynamics: insight from an NMR study.
  J Phys Chem B, 112, 14312-14318.  
18713896 C.M.Crowder (2008).
Does natural selection explain the universal response of metazoans to volatile anesthetics?
  Anesth Analg, 107, 862-863.  
18264582 H.Fraga (2008).
Firefly luminescence: a historical perspective and recent developments.
  Photochem Photobiol Sci, 7, 146-158.  
18713893 J.M.Sonner (2008).
A hypothesis on the origin and evolution of the response to inhaled anesthetics.
  Anesth Analg, 107, 849-854.  
18309312 P.D.Dobson, and D.B.Kell (2008).
Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?
  Nat Rev Drug Discov, 7, 205-220.  
18449184 R.Eckenhoff, W.Zheng, and M.Kelz (2008).
From anesthetic mechanisms research to drug discovery.
  Clin Pharmacol Ther, 84, 144-148.  
18713895 R.G.Eckenhoff (2008).
Why can all of biology be anesthetized?
  Anesth Analg, 107, 859-861.  
17993502 V.Bondarenko, V.E.Yushmanov, Y.Xu, and P.Tang (2008).
NMR study of general anesthetic interaction with nAChR beta2 subunit.
  Biophys J, 94, 1681-1688.  
17513367 A.Szarecka, Y.Xu, and P.Tang (2007).
Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses.
  Biophys J, 93, 1895-1905.  
17565494 C.Etchebest, C.Benros, A.Bornot, A.C.Camproux, and A.G.de Brevern (2007).
A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.
  Eur Biophys J, 36, 1059-1069.  
18042866 C.W.Buffington, M.J.Laster, K.Jankowska, and E.I.Eger (2007).
Concentrations of isoflurane exceeding those used clinically slightly increase the affinity of methane, but not toluene, for water.
  Anesth Analg, 105, 1675.  
17242087 E.J.Bertaccini, J.R.Trudell, and N.P.Franks (2007).
The common chemical motifs within anesthetic binding sites.
  Anesth Analg, 104, 318-324.  
17293400 T.Heimburg, and A.D.Jackson (2007).
The thermodynamics of general anesthesia.
  Biophys J, 92, 3159-3165.  
17003895 A.Wlodarczyk, P.F.McMillan, and S.A.Greenfield (2006).
High pressure effects in anaesthesia and narcosis.
  Chem Soc Rev, 35, 890-898.  
16877516 J.H.Streiff, T.W.Allen, E.Atanasova, N.Juranic, S.Macura, A.R.Penheiter, and K.A.Jones (2006).
Prediction of volatile anesthetic binding sites in proteins.
  Biophys J, 91, 3405-3414.  
16361257 M.T.Roberts, R.Phelan, B.S.Erlichman, R.N.Pillai, L.Ma, G.F.Lopreato, and S.J.Mihic (2006).
Occupancy of a single anesthetic binding pocket is sufficient to enhance glycine receptor function.
  J Biol Chem, 281, 3305-3311.  
16877515 S.Vemparala, L.Saiz, R.G.Eckenhoff, and M.L.Klein (2006).
Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles.
  Biophys J, 91, 2815-2825.  
16541080 T.Nakatsu, S.Ichiyama, J.Hiratake, A.Saldanha, N.Kobashi, K.Sakata, and H.Kato (2006).
Structural basis for the spectral difference in luciferase bioluminescence.
  Nature, 440, 372-376.
PDB codes: 2d1q 2d1r 2d1s 2d1t
16124832 V.R.Viviani, T.L.Oehlmeyer, F.G.Arnoldi, and M.R.Brochetto-Braga (2005).
A new firefly luciferase with bimodal spectrum: identification of structural determinants of spectral pH-sensitivity in firefly luciferases.
  Photochem Photobiol, 81, 843-848.  
14745295 J.R.Trudell, and R.A.Harris (2004).
Are sobriety and consciousness determined by water in protein cavities?
  Alcohol Clin Exp Res, 28, 1-3.  
15220795 N.P.Franks, and W.R.Lieb (2004).
Seeing the light: protein theories of general anesthesia. 1984.
  Anesthesiology, 101, 235-237.  
15487945 R.Finking, and M.A.Marahiel (2004).
Biosynthesis of nonribosomal peptides1.
  Annu Rev Microbiol, 58, 453-488.  
12685663 A.Kitayama, H.Yoshizaki, Y.Ohmiya, H.Ueda, and T.Nagamune (2003).
Creation of a thermostable firefly luciferase with pH-insensitive luminescent color.
  Photochem Photobiol, 77, 333-338.  
12967348 S.Rocha, K.J.Campbell, K.C.Roche, and N.D.Perkins (2003).
The p53-inhibitor pifithrin-alpha inhibits firefly luciferase activity in vivo and in vitro.
  BMC Mol Biol, 4, 9.  
12881720 S.W.Kruse, R.Zhao, D.P.Smith, and D.N.Jones (2003).
Structure of a specific alcohol-binding site defined by the odorant binding protein LUSH from Drosophila melanogaster.
  Nat Struct Biol, 10, 694-700.
PDB codes: 1oof 1oog 1ooh 1ooi
12221282 J.J.May, N.Kessler, M.A.Marahiel, and M.T.Stubbs (2002).
Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases.
  Proc Natl Acad Sci U S A, 99, 12120-12125.
PDB codes: 1md9 1mdb 1mdf
12596852 N.Hattori, N.Kajiyama, M.Maeda, and S.Murakami (2002).
Mutant luciferase enzymes from fireflies with increased resistance to benzalkonium chloride.
  Biosci Biotechnol Biochem, 66, 2587-2593.  
12202367 P.Tang, P.K.Mandal, and M.Zegarra (2002).
Effects of volatile anesthetic on channel structure of gramicidin A.
  Biophys J, 83, 1413-1420.  
12007636 X.C.Wang, J.Yang, W.Huang, L.He, J.T.Yu, Q.S.Lin, W.Li, and H.M.Zhou (2002).
Effects of removal of the N-terminal amino acid residues on the activity and conformation of firefly luciferase.
  Int J Biochem Cell Biol, 34, 983-991.  
11327861 B.R.Branchini, R.A.Magyar, M.H.Murtiashaw, and N.C.Portier (2001).
The role of active site residue arginine 218 in firefly luciferase bioluminescence.
  Biochemistry, 40, 2410-2418.  
11747900 M.D.Krasowski, K.Nishikawa, N.Nikolaeva, A.Lin, and N.L.Harrison (2001).
Methionine 286 in transmembrane domain 3 of the GABAA receptor beta subunit controls a binding cavity for propofol and other alkylphenol general anesthetics.
  Neuropharmacology, 41, 952-964.  
11170198 R.G.Eckenhoff, J.W.Tanner, and P.A.Liebman (2001).
Cooperative binding of inhaled anesthetics and ATP to firefly luciferase.
  Proteins, 42, 436-441.  
11682406 Y.Zhang, C.R.Stabernack, R.Dutton, J.Sonner, J.R.Trudell, S.J.Mihic, T.Yamakura, R.A.Harris, D.Gong, and E.I.Eger (2001).
Luciferase as a model for the site of inhaled anesthetic action.
  Anesth Analg, 93, 1246-1252.  
10781301 D.E.Raines (2000).
Perturbation of lipid and protein structure by general anesthetics: how little is too little?
  Anesthesiology, 92, 1492-1494.  
10683198 M.D.Krasowski, and N.L.Harrison (2000).
The actions of ether, alcohol and alkane general anaesthetics on GABAA and glycine receptors and the effects of TM2 and TM3 mutations.
  Br J Pharmacol, 129, 731-743.  
10908659 M.P.Mascia, J.R.Trudell, and R.A.Harris (2000).
Specific binding sites for alcohols and anesthetics on ligand-gated ion channels.
  Proc Natl Acad Sci U S A, 97, 9305-9310.  
10754611 N.L.Harrison (2000).
Ion channels take center stage: twin spotlights on two anesthetic targets.
  Anesthesiology, 92, 936-938.  
10653787 Y.Xu, T.Seto, P.Tang, and L.Firestone (2000).
NMR study of volatile anesthetic binding to nicotinic acetylcholine receptors.
  Biophys J, 78, 746-751.  
10357351 E.I.Eger, M.J.Halsey, R.A.Harris, D.D.Koblin, A.Pohorille, J.C.Sewell, J.M.Sonner, and J.R.Trudell (1999).
Hypothesis: volatile anesthetics produce immobility by acting on two sites approximately five carbon atoms apart.
  Anesth Analg, 88, 1395-1400.  
10487207 M.D.Krasowski, and N.L.Harrison (1999).
General anaesthetic actions on ligand-gated ion channels.
  Cell Mol Life Sci, 55, 1278-1303.  
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.