2vtb: Difference between revisions

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[[Image:2vtb.png|left|200px]]


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==Structure of cryptochrome 3 - DNA complex==
The line below this paragraph, containing "STRUCTURE_2vtb", creates the "Structure Box" on the page.
<StructureSection load='2vtb' size='340' side='right'caption='[[2vtb]], [[Resolution|resolution]] 2.01&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'>[[2vtb]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VTB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VTB 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]] 2.01&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MHF:5,10-METHENYL-6,7,8-TRIHYDROFOLIC+ACID'>MHF</scene>, <scene name='pdbligand=TCP:5-METHYLTHYMIDINE'>TCP</scene></td></tr>
{{STRUCTURE_2vtb|  PDB=2vtb  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vtb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vtb OCA], [https://pdbe.org/2vtb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vtb RCSB], [https://www.ebi.ac.uk/pdbsum/2vtb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vtb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CRYD_ARATH CRYD_ARATH] May have a photoreceptor function. Binds ss- and ds-DNA in a sequence non-specific manner. Has a photolyase activity specific for cyclobutane pyrimidine dimers in ssDNA.<ref>PMID:17062752</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/vt/2vtb_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=2vtb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or for signaling, respectively. Very recently, it was shown that members of the DASH cryptochrome subclade repair specifically cyclobutane pyrimidine dimers (CPDs) in UV-damaged single-stranded DNA. Here, we report the crystal structure of Arabidopsis cryptochrome 3 with an in-situ-repaired CPD substrate in single-stranded DNA. The structure shows a binding mode similar to that of conventional DNA photolyases. Furthermore, CPD lesions in double-stranded DNA are bound and repaired with similar efficiency as in single-stranded DNA if the CPD lesion is present in a loop structure. Together, these data reveal that DASH cryptochromes catalyze light-driven DNA repair like conventional photolyases but lack an efficient flipping mechanism for interaction with CPD lesions within duplex DNA.


===STRUCTURE OF CRYPTOCHROME 3 - DNA COMPLEX===
Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.,Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen LO Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21023-7. Epub 2008 Dec 12. PMID:19074258<ref>PMID:19074258</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2vtb" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19074258}}, adds the Publication Abstract to the page
*[[Cryptochrome 3D structures|Cryptochrome 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19074258 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19074258}}
__TOC__
 
</StructureSection>
==About this Structure==
[[2vtb]] is a 12 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=2VTB OCA].
 
==Reference==
<ref group="xtra">PMID:019074258</ref><ref group="xtra">PMID:017188299</ref><references group="xtra"/>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: Deoxyribodipyrimidine photo-lyase]]
[[Category: Homo sapiens]]
[[Category: Batschauer, A.]]
[[Category: Large Structures]]
[[Category: Carell, T.]]
[[Category: Batschauer A]]
[[Category: Essen, L O.]]
[[Category: Carell T]]
[[Category: Hennecke, U.]]
[[Category: Essen L-O]]
[[Category: Klar, T.]]
[[Category: Hennecke U]]
[[Category: Pokorny, R.]]
[[Category: Klar T]]
[[Category: Chloroplast]]
[[Category: Pokorny R]]
[[Category: Chromophore]]
[[Category: Cryptochrome]]
[[Category: Cyclobutane-pyrimidine dimer]]
[[Category: Dna]]
[[Category: Dna-binding]]
[[Category: Fad]]
[[Category: Flavin adenine dinucleotide]]
[[Category: Flavoprotein]]
[[Category: Lyase dna complex]]
[[Category: Lyase-dna complex]]
[[Category: Mitochondrion]]
[[Category: Photolyase]]
[[Category: Single-stranded dna]]
[[Category: Transit peptide]]

Latest revision as of 18:31, 13 December 2023

Structure of cryptochrome 3 - DNA complexStructure of cryptochrome 3 - DNA complex

Structural highlights

2vtb is a 12 chain structure with sequence from Arabidopsis thaliana and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.01Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CRYD_ARATH May have a photoreceptor function. Binds ss- and ds-DNA in a sequence non-specific manner. Has a photolyase activity specific for cyclobutane pyrimidine dimers in ssDNA.[1]

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

DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or for signaling, respectively. Very recently, it was shown that members of the DASH cryptochrome subclade repair specifically cyclobutane pyrimidine dimers (CPDs) in UV-damaged single-stranded DNA. Here, we report the crystal structure of Arabidopsis cryptochrome 3 with an in-situ-repaired CPD substrate in single-stranded DNA. The structure shows a binding mode similar to that of conventional DNA photolyases. Furthermore, CPD lesions in double-stranded DNA are bound and repaired with similar efficiency as in single-stranded DNA if the CPD lesion is present in a loop structure. Together, these data reveal that DASH cryptochromes catalyze light-driven DNA repair like conventional photolyases but lack an efficient flipping mechanism for interaction with CPD lesions within duplex DNA.

Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.,Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen LO Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21023-7. Epub 2008 Dec 12. PMID:19074258[2]

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

See Also

References

  1. ↑ Selby CP, Sancar A. A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17696-700. Epub 2006 Oct 24. PMID:17062752 doi:http://dx.doi.org/0607993103
  2. ↑ Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen LO. Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21023-7. Epub 2008 Dec 12. PMID:19074258

2vtb, resolution 2.01Å

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