1vas: Difference between revisions

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[[Image:1vas.gif|left|200px]]


{{Structure
==ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION==
|PDB= 1vas |SIZE=350|CAPTION= <scene name='initialview01'>1vas</scene>, resolution 2.750&Aring;
<StructureSection load='1vas' size='340' side='right'caption='[[1vas]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1vas]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. The July 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Thymine Dimers''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_7 10.2210/rcsb_pdb/mom_2007_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VAS FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75&#8491;</td></tr>
|GENE= DENV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4])
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vas OCA], [https://pdbe.org/1vas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vas RCSB], [https://www.ebi.ac.uk/pdbsum/1vas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vas ProSAT]</span></td></tr>
}}
</table>
== Function ==
[https://www.uniprot.org/uniprot/END5_BPT4 END5_BPT4]
== 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/va/1vas_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=1vas ConSurf].
<div style="clear:both"></div>


'''ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION'''
==See Also==
 
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
T4 endonuclease V is a DNA repair enzyme from bacteriophage T4 that catalyzes the first reaction step of the pyrimidine dimer-specific base excision repair pathway. The crystal structure of this enzyme complexed with a duplex DNA substrate, containing a thymine dimer, has been determined at 2.75 A resolution. The atomic structure of the complex reveals the unique conformation of the DNA duplex, which exhibits a sharp kink with a 60 degree inclination at the central thymine dimer. The adenine base complementary to the 5' side of the thymine dimer is completely flipped out of the DNA duplex and trapped in a cavity on the protein surface. These structural features allow an understanding of the catalytic mechanism and implicate a general mechanism of how other repair enzymes recognize damaged DNA duplexes.
[[Category: Escherichia virus T4]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: RCSB PDB Molecule of the Month]]
1VAS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. The following page contains interesting information on the relation of 1VAS with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VAS OCA].
 
==Reference==
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition., Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K, Cell. 1995 Dec 1;83(5):773-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8521494 8521494]
[[Category: Bacteriophage t4]]
[[Category: Single protein]]
[[Category: Thymine Dimers]]
[[Category: Thymine Dimers]]
[[Category: Ariyoshi, M.]]
[[Category: Ariyoshi M]]
[[Category: Iwai, S.]]
[[Category: Iwai S]]
[[Category: Kashiwagi, T.]]
[[Category: Kashiwagi T]]
[[Category: Mikami, Y.]]
[[Category: Mikami Y]]
[[Category: Morikawa, K.]]
[[Category: Morikawa K]]
[[Category: Ohtsuka, E.]]
[[Category: Ohtsuka E]]
[[Category: Vassylyev, D G.]]
[[Category: Vassylyev DG]]
[[Category: double helix]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:43:03 2008''

Latest revision as of 11:45, 14 February 2024

ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITIONATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION

Structural highlights

1vas is a 3 chain structure with sequence from Escherichia virus T4. The July 2007 RCSB PDB Molecule of the Month feature on Thymine Dimers by David S. Goodsell is 10.2210/rcsb_pdb/mom_2007_7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.75Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

END5_BPT4

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1vas, resolution 2.75Å

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