1vpr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_1vpr", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
Current revision (07:34, 30 October 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1vpr.png|left|200px]]
 
-
<!--
+
==Crystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum==
-
The line below this paragraph, containing "STRUCTURE_1vpr", creates the "Structure Box" on the page.
+
<StructureSection load='1vpr' size='340' side='right'caption='[[1vpr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</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>
-
{{STRUCTURE_1vpr| PDB=1vpr | SCENE= }}
+
<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>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vp/1vpr_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vpr ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 luciferase domain from the dinoflagellate Lingulodinium polyedrum===
+
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<ref>PMID:15665092</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_15665092}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1vpr" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15665092 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_15665092}}
+
-
 
+
-
==About this Structure==
+
-
[[1vpr]] is a 1 chain structure of [[Dinoflagellate luciferase]] and [[Luciferase]] with sequence from [http://en.wikipedia.org/wiki/Lingulodinium_polyedrum Lingulodinium polyedrum]. The June 2006 RCSB PDB [http://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 [http://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].
+
==See Also==
==See Also==
*[[Dinoflagellate luciferase|Dinoflagellate luciferase]]
*[[Dinoflagellate luciferase|Dinoflagellate luciferase]]
-
*[[Luciferase|Luciferase]]
+
*[[Luciferase 3D structures|Luciferase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:015665092</ref><ref group="xtra">PMID:012657805</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Lingulodinium polyedrum]]
+
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Lingulodinium polyedra]]
[[Category: Luciferase]]
[[Category: Luciferase]]
[[Category: RCSB PDB Molecule of the Month]]
[[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: Luciferase]]
+
-
[[Category: Luminescent protein]]
+
-
[[Category: Ph regulation]]
+

Current revision

Crystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum

PDB ID 1vpr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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