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.

3fy4

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 01:14, 9 February 2016

(6-4) Photolyase Crystal Structure

Structural highlights

3fy4 is a 3 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Gene:	6-4 PHOTOLYASE, UVR3 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[UVR3_ARATH] Involved in repair of UV radiation-induced DNA damage. Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone photoproduct (6-4 products). Binds specifically to DNA containing 6-4 products and repairs these lesions in a visible light-dependent manner. Not required for repair of cyclobutane pyrimidine dimer (CPD).^[1] ^[2]

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

Homologous flavoproteins from the photolyase (PHR)/cryptochrome (CRY) family use the FAD cofactor in PHRs to catalyze DNA repair and in CRYs to tune the circadian clock and control development. To help address how PHR/CRY members achieve these diverse functions, we determined the crystallographic structure of Arabidopsis thaliana (6-4) PHR (UVR3), which is strikingly (>65%) similar in sequence to human circadian clock CRYs. The structure reveals a substrate-binding cavity specific for the UV-induced DNA lesion, (6-4) photoproduct, and cofactor binding sites different from those of bacterial PHRs and consistent with distinct mechanisms for activities and regulation. Mutational analyses were combined with this prototypic structure for the (6-4) PHR/clock CRY cluster to identify structural and functional motifs: phosphate-binding and Pro-Lys-Leu protrusion motifs constricting access to the substrate-binding cavity above FAD, sulfur loop near the external end of the Trp electron-transfer pathway, and previously undefined C-terminal helix. Our results provide a detailed, unified framework for investigations of (6-4) PHRs and the mammalian CRYs. Conservation of key residues and motifs controlling FAD access and activities suggests that regulation of FAD redox properties and radical stability is essential not only for (6-4) photoproduct DNA repair, but also for circadian clock-regulating CRY functions. The structural and functional results reported here elucidate archetypal relationships within this flavoprotein family and suggest how PHRs and CRYs use local residue and cofactor tuning, rather than larger structural modifications, to achieve their diverse functions encompassing DNA repair, plant growth and development, and circadian clock regulation.

Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes.,Hitomi K, Ditacchio L, Arvai AS, Yamamoto J, Kim ST, Todo T, Tainer JA, Iwai S, Panda S, Getzoff ED Proc Natl Acad Sci U S A. 2009 Apr 9. PMID:19359474^[3]

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

References

↑ Schleicher E, Hitomi K, Kay CW, Getzoff ED, Todo T, Weber S. Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J Biol Chem. 2007 Feb 16;282(7):4738-47. Epub 2006 Dec 12. PMID:17164245 doi:http://dx.doi.org/10.1074/jbc.M604734200
↑ Nakajima S, Sugiyama M, Iwai S, Hitomi K, Otoshi E, Kim ST, Jiang CZ, Todo T, Britt AB, Yamamoto K. Cloning and characterization of a gene (UVR3) required for photorepair of 6-4 photoproducts in Arabidopsis thaliana. Nucleic Acids Res. 1998 Jan 15;26(2):638-44. PMID:9421527
↑ Hitomi K, Ditacchio L, Arvai AS, Yamamoto J, Kim ST, Todo T, Tainer JA, Iwai S, Panda S, Getzoff ED. Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc Natl Acad Sci U S A. 2009 Apr 9. PMID:19359474

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3fy4"

@@ Line 2: / Line 2: @@
 <StructureSection load='3fy4' size='340' side='right' caption='[[3fy4]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fy4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FY4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fy4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FY4 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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">6-4 PHOTOLYASE, UVR3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">6-4 PHOTOLYASE, UVR3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=3fy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fy4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fy4 RCSB], [http://www.ebi.ac.uk/pdbsum/3fy4 PDBsum]</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=3fy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fy4 OCA], [http://pdbe.org/3fy4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fy4 RCSB], [http://www.ebi.ac.uk/pdbsum/3fy4 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/O48652_ARATH O48652_ARATH]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone photoproduct (6-4 products). Binds specifically to DNA containing 6-4 products and repairs these lesions in a visible light-dependent manner. Not required for repair of cyclobutane pyrimidine dimer (CPD).<ref>PMID:17164245</ref> <ref>PMID:9421527</ref>
+[[http://www.uniprot.org/uniprot/UVR3_ARATH UVR3_ARATH]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone photoproduct (6-4 products). Binds specifically to DNA containing 6-4 products and repairs these lesions in a visible light-dependent manner. Not required for repair of cyclobutane pyrimidine dimer (CPD).<ref>PMID:17164245</ref> <ref>PMID:9421527</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 17: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3fy4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3fy4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: Arvai, A S]]
 [[Category: Getzoff, E D]]

3fy4

From Proteopedia

Revision as of 01:14, 9 February 2016

(6-4) Photolyase Crystal Structure

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox