1tez: Difference between revisions

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~~{{Seed}}~~

~~[[Image:1tez.png|left|200px]]~~

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==COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS==

~~The line below this paragraph~~, ~~containing~~ "~~STRUCTURE_1tez~~"~~, creates the~~ "~~Structure Box~~" ~~on the page~~.

~~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'>[[1tez]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_6301 Synechococcus elongatus PCC 6301] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TEZ 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]] 1.8Å</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=HDF:8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE'>HDF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TCP:5-METHYLTHYMIDINE'>TCP</scene></td></tr>

~~{{STRUCTURE_1tez| PDB~~=~~1tez | SCENE~~= }}

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tez OCA], [https://pdbe.org/1tez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tez RCSB], [https://www.ebi.ac.uk/pdbsum/1tez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tez ProSAT]</span></td></tr>

</table>

== 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 ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/te/1tez_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1tez ConSurf].

== Publication Abstract from PubMed ==

DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.

~~===COMPLEX BETWEEN~~ DNA ~~AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS===~~

Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair.,Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO Science. 2004 Dec 3;306(5702):1789-93. PMID:15576622<ref>PMID:15576622</ref>

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

~~<!--~~

</div>

~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_15576622}}, adds~~ the ~~Publication Abstract to the page~~

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 15576622 is the PubMed ID number~~.

== References ==

-->

~~{{ABSTRACT_PUBMED_15576622}}~~

__TOC__

</StructureSection>

==~~About this Structure==~~

[[Category: Large Structures]]

~~1TEZ 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=1TEZ OCA].~~

[[Category: Synechococcus elongatus PCC 6301]]

[[Category: Synthetic construct]]

==~~Reference~~==

[[Category: Carell T]]

Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair., Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO, Science. 2004 Dec 3;306(5702):1789-93. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/15576622 15576622]~~

[[Category: Essen L-O]]

[[Category: Klar T]]

~~Crystal structure of DNA photolyase from Anacystis nidulans., Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K, Nat Struct Biol. 1997 Nov;4(11):887-91. PMID:[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/9360600 9360600]~~

[[Category: Mees A]]

[[Category: ~~Deoxyribodipyrimidine photo-lyase~~]]

[[Category: ~~Single protein~~]]

[[Category: ~~Synechococcus sp.~~]]

[[Category: Carell, T.]]

[[Category: Essen, L O.]]

[[Category: Klar, T.]]

[[Category: Mees, A~~.]]~~

~~[[Category: Dna repair~~]]

~~[[Category: Light-driven electron transfer]]~~

~~[[Category: Photolyase]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:42:40 2008''~~

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@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1tez.png|left|200px]]
-<!--
+==COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS==
-The line below this paragraph, containing "STRUCTURE_1tez", creates the "Structure Box" on the page.
+<StructureSection load='1tez' size='340' side='right'caption='[[1tez]], [[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'>[[1tez]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_6301 Synechococcus elongatus PCC 6301] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TEZ 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HDF:8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE'>HDF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TCP:5-METHYLTHYMIDINE'>TCP</scene></td></tr>
-{{STRUCTURE_1tez|  PDB=1tez  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tez OCA], [https://pdbe.org/1tez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tez RCSB], [https://www.ebi.ac.uk/pdbsum/1tez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tez ProSAT]</span></td></tr>
+</table>
+== 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 ==
+[[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/te/1tez_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1tez ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.
-===COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS===
+Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair.,Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO Science. 2004 Dec 3;306(5702):1789-93. PMID:15576622<ref>PMID:15576622</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_15576622}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1tez" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15576622 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15576622}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-TEZ 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=1TEZ OCA].
+[[Category: Synechococcus elongatus PCC 6301]]
+[[Category: Synthetic construct]]
-==Reference==
+[[Category: Carell T]]
-Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair., Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO, Science. 2004 Dec 3;306(5702):1789-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15576622 15576622]
+[[Category: Essen L-O]]
+[[Category: Klar T]]
-Crystal structure of DNA photolyase from Anacystis nidulans., Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K, Nat Struct Biol. 1997 Nov;4(11):887-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9360600 9360600]
+[[Category: Mees A]]
-[[Category: Deoxyribodipyrimidine photo-lyase]]
-[[Category: Single protein]]
-[[Category: Synechococcus sp.]]
-[[Category: Carell, T.]]
-[[Category: Essen, L O.]]
-[[Category: Klar, T.]]
-[[Category: Mees, A.]]
-[[Category: Dna repair]]
-[[Category: Light-driven electron transfer]]
-[[Category: Photolyase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:42:40 2008''