1vas: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='1vas' size='340' side='right'caption='[[1vas]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
<StructureSection load='1vas' size='340' side='right'caption='[[1vas]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1vas]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. 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>
<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>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DENV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
</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>
<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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/END5_BPT4 END5_BPT4]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 17: Line 19:
</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:8521494<ref>PMID:8521494</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1vas" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bpt4]]
[[Category: Escherichia virus T4]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[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: Hydrolase-dna complex]]
[[Category: Protein-dna complex]]

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

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1vas&oldid=4055978"