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.


4cdn

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 3: Line 3:
<StructureSection load='4cdn' size='340' side='right'caption='[[4cdn]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='4cdn' size='340' side='right'caption='[[4cdn]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4cdn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metma Metma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CDN FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4cdn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei_Go1 Methanosarcina mazei Go1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CDN FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FO1:1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL'>FO1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+
</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=FO1:1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL'>FO1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4cdm|4cdm]]</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=4cdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cdn OCA], [https://pdbe.org/4cdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cdn RCSB], [https://www.ebi.ac.uk/pdbsum/4cdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cdn ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4cdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cdn OCA], [http://pdbe.org/4cdn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cdn RCSB], [http://www.ebi.ac.uk/pdbsum/4cdn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cdn ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[[https://www.uniprot.org/uniprot/Q8PYK9_METMA Q8PYK9_METMA]]
-
Light-harvesting and resonance energy transfer to the catalytic FAD cofactor are key roles for the antenna chromophores of light-driven DNA photolyases, which remove UV-induced DNA lesions. So far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. Despite a common protein topology, structural analysis of the distantly related class II photolyase from the archaeon Methanosarcina mazei (MmCPDII) as well as plantal orthologues indicated several differences in terms of DNA- and FAD-binding and electron transfer pathways. For MmCPDII we identify 8-hydroxydeazaflavin (8-HDF) as cognate antenna by in vitro and in vivo reconstitution, whereas the higher plant class II photolyase from Arabidopsis thaliana fails to bind any of the known chromophores. According to the 1.9 Angstrom structure of the MmCPDII/8-HDF complex its antenna binding site differs from other members of the photolyase-cryptochrome superfamily by an antenna loop that changes its conformation by 12 Angstrom upon 8-HDF binding. Additionally, so-called N- and C-motifs contribute as conserved elements to the binding of deprotonated 8-HDF and allow predicting 8-HDF binding for most of the class II photolyases in the whole phylome. The 8-HDF antenna is used throughout the viridiplantae ranging from green micro-algae to bryophyta and pteridophyta, i. e. mosses and ferns, but interestingly not in higher plants. Overall, we suggest that 8-hydroxydeazaflavin is a crucial factor for the survival of most higher eukaryotes which depend on class II photolyases to struggle with the genotoxic effects of solar UV-exposure.
+
-
 
+
-
Structural and Evolutionary Aspects of Antenna Chromophore Usage by Class II Photolyases.,Kiontke S, Gnau P, Haselsberger R, Batschauer A, Essen LO J Biol Chem. 2014 May 21. pii: jbc.M113.542431. PMID:24849603<ref>PMID:24849603</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4cdn" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Deoxyribodipyrimidine photo-lyase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Metma]]
+
[[Category: Methanosarcina mazei Go1]]
-
[[Category: Batschauer, A]]
+
[[Category: Batschauer A]]
-
[[Category: Essen, L O]]
+
[[Category: Essen L-O]]
-
[[Category: Kiontke, S]]
+
[[Category: Kiontke S]]
-
[[Category: 8-hdf]]
+
-
[[Category: Antenna chromophore]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Fad]]
+
-
[[Category: Lyase]]
+
-
[[Category: Methanosarcina mazei]]
+
-
[[Category: Photolyase]]
+

Revision as of 17:40, 7 September 2022

Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-HDF antenna chromophore

PDB ID 4cdn

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/4cdn"
Personal tools