This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1owm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:28, 13 March 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1owm.jpg|left|200px]]
 
-
<!--
+
==DATA1:DNA photolyase / received X-rays dose 1.2 exp15 photons/mm2==
-
The line below this paragraph, containing "STRUCTURE_1owm", creates the "Structure Box" on the page.
+
<StructureSection load='1owm' size='340' side='right'caption='[[1owm]], [[Resolution|resolution]] 2.30&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'>[[1owm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_6301 Synechococcus elongatus PCC 6301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OWM 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]] 2.3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
{{STRUCTURE_1owm| PDB=1owm | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1owm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1owm OCA], [https://pdbe.org/1owm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1owm RCSB], [https://www.ebi.ac.uk/pdbsum/1owm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1owm ProSAT]</span></td></tr>
-
 
+
</table>
-
'''DATA1:DNA photolyase / received X-rays dose 1.2 exp15 photons/mm2'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PHR_SYNP6 PHR_SYNP6] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
DNA photolyase is a unique flavoenzyme that repairs UV-induced DNA lesions using the energy of visible light. Anacystis nidulans photolyase contains a light-harvesting chromophore, 8-hydroxy-5-deazaflavin (8-HDF), and flavin adenine dinucleotide (FAD) which, in contrast to the 8-HDF chromophore, is indispensable for catalytic activity. This work reports the crystallization and structure at 1.8 A resolution of DNA photolyase devoid of its 8-HDF chromophore (apophotolyase). The overall three-dimensional structure is similar to that of the holoenzyme, indicating that the presence of 8-HDF is not essential for the correct folding of the enzyme. Structural changes include an additional phosphate group, a different conformation for Arg11 and slight rearrangements of Met47, Asp101 and Asp382, which replace part of the 8-HDF molecule in the chromophore-binding pocket. The apophotolyase can be efficiently reconstituted with synthetic 8-hydroxy-5-deazariboflavin, despite the orientation of Arg11 and the presence of the phosphate group in the 8-HDF pocket. Red light or X-rays reduced the FAD chromophore in apophotolyase crystals, as observed by single-crystal spectrophotometry. The structural effects of FAD reduction were determined by comparison of three data sets that were successively collected at 100 K, while the degree of reduction was monitored online by changes in the light absorption of the crystals. X-ray-induced conformational changes were confined to the active site of the protein. They include sub-angstrom movements of the O(2) and N(5) atoms of the flavin group as well as the O(delta) atoms of the surrounding amino acids Asp380 and Asn386.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ow/1owm_consurf.spt"</scriptWhenChecked>
-
1OWM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OWM OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction., Kort R, Komori H, Adachi S, Miki K, Eker A, Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1205-13. Epub 2004, Jun 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15213381 15213381]
+
</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=1owm ConSurf].
-
[[Category: Deoxyribodipyrimidine photo-lyase]]
+
<div style="clear:both"></div>
-
[[Category: Single protein]]
+
__TOC__
-
[[Category: Synechococcus sp.]]
+
</StructureSection>
-
[[Category: Adachi, S.]]
+
[[Category: Large Structures]]
-
[[Category: Eker, A.]]
+
[[Category: Synechococcus elongatus PCC 6301]]
-
[[Category: Komori, H.]]
+
[[Category: Adachi S]]
-
[[Category: Kort, R.]]
+
[[Category: Eker A]]
-
[[Category: Miki, K.]]
+
[[Category: Komori H]]
-
[[Category: Dna repair]]
+
[[Category: Kort R]]
-
[[Category: Flavin enzyme]]
+
[[Category: Miki K]]
-
[[Category: Photoreactivating enzyme]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:22:14 2008''
+

Current revision

DATA1:DNA photolyase / received X-rays dose 1.2 exp15 photons/mm2

PDB ID 1owm

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/1owm"
Personal tools