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1vpr

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Current revision

Crystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum

Structural highlights

1vpr is a 1 chain structure with sequence from Lingulodinium polyedra. The June 2006 RCSB PDB Molecule of the Month feature on Luciferase by David S. Goodsell is 10.2210/rcsb_pdb/mom_2006_6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LUCIF_LINPO Emits blue light flashes with a wavelength of 475 nm during the night phase.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The luciferase of Lingulodinium polyedrum, a marine bioluminescent dinoflagellate, consists of three similar but not identical domains in a single polypeptide. Each encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived open tetrapyrrole (dinoflagellate luciferin) to produce blue light. These domains share no sequence similarity with any other in the GenBank database and no structural or motif similarity with any other luciferase. We report here the 1.8-A crystal structure of the third domain, D3, at pH 8, and a mechanism for its activity regulation by pH. D3 consists of two major structural elements: a beta-barrel pocket putatively for substrate binding and catalysis and a regulatory three-helix bundle. N-terminal histidine residues previously shown to regulate activity by pH are at the interface of the helices in the bundle. Molecular dynamics calculations indicate that, in response to changes in pH, these histidines could trigger a large molecular motion of the bundle, thereby exposing the active site to the substrate.

Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole.,Schultz LW, Liu L, Cegielski M, Hastings JW Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1378-83. Epub 2005 Jan 21. PMID:15665092^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schultz LW, Liu L, Cegielski M, Hastings JW. Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1378-83. Epub 2005 Jan 21. PMID:15665092
↑ Dunlap JC, Hastings JW. The biological clock in Gonyaulax controls luciferase activity by regulating turnover. J Biol Chem. 1981 Oct 25;256(20):10509-18. PMID:7197271
↑ Bae YM, Hastings JW. Cloning, sequencing and expression of dinoflagellate luciferase DNA from a marine alga, Gonyaulax polyedra. Biochim Biophys Acta. 1994 Oct 18;1219(2):449-56. PMID:7918642
↑ Schultz LW, Liu L, Cegielski M, Hastings JW. Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1378-83. Epub 2005 Jan 21. PMID:15665092

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vpr"

@@ Line 3: / Line 3: @@
 <StructureSection load='1vpr' size='340' side='right'caption='[[1vpr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vpr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dinoflagellate Dinoflagellate]. The June 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Luciferase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_6 10.2210/rcsb_pdb/mom_2006_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VPR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vpr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lingulodinium_polyedra Lingulodinium polyedra]. The June 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Luciferase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_6 10.2210/rcsb_pdb/mom_2006_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VPR FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vpr OCA], [https://pdbe.org/1vpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vpr RCSB], [https://www.ebi.ac.uk/pdbsum/1vpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vpr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/LUCIF_LINPO LUCIF_LINPO]] Emits blue light flashes with a wavelength of 475 nm during the night phase.<ref>PMID:15665092</ref> <ref>PMID:7197271</ref> <ref>PMID:7918642</ref>
+[https://www.uniprot.org/uniprot/LUCIF_LINPO LUCIF_LINPO] Emits blue light flashes with a wavelength of 475 nm during the night phase.<ref>PMID:15665092</ref> <ref>PMID:7197271</ref> <ref>PMID:7918642</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Dinoflagellate]]
 [[Category: Large Structures]]
+[[Category: Lingulodinium polyedra]]
 [[Category: Luciferase]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Cegielski, M]]
+[[Category: Cegielski M]]
-[[Category: Hastings, J W]]
+[[Category: Hastings JW]]
-[[Category: Liu, L]]
+[[Category: Liu L]]
-[[Category: Schultz, L W]]
+[[Category: Schultz LW]]
-[[Category: Beta barrel]]
-[[Category: Fatty acid binding protein]]
-[[Category: Lipocalin]]
-[[Category: Luminescent protein]]
-[[Category: Ph regulation]]

1vpr

From Proteopedia

Current revision

Crystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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