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.


1vas

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 4: Line 4:
|PDB= 1vas |SIZE=350|CAPTION= <scene name='initialview01'>1vas</scene>, resolution 2.750&Aring;
|PDB= 1vas |SIZE=350|CAPTION= <scene name='initialview01'>1vas</scene>, resolution 2.750&Aring;
|SITE=
|SITE=
-
|LIGAND=
+
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
|ACTIVITY=
|ACTIVITY=
-
|GENE= DENV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4])
+
|GENE= DENV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
 +
|DOMAIN=
 +
|RELATEDENTRY=
 +
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vas OCA], [http://www.ebi.ac.uk/pdbsum/1vas PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vas RCSB]</span>
}}
}}
Line 16: Line 19:
==About this Structure==
==About this Structure==
-
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].
+
1VAS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage 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==
==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]
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: Enterobacteria phage t4]]
[[Category: Single protein]]
[[Category: Single protein]]
[[Category: Thymine Dimers]]
[[Category: Thymine Dimers]]
Line 33: Line 36:
[[Category: protein-dna complex]]
[[Category: protein-dna complex]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:43:03 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:21:47 2008''

Revision as of 21:21, 30 March 2008

Image:1vas.gif


PDB ID 1vas

Drag the structure with the mouse to rotate
, resolution 2.750Å
Ligands: , , ,
Gene: DENV (Enterobacteria phage T4)
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



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


Overview

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.

About this Structure

1VAS is a Single protein structure of sequence from Enterobacteria phage t4. The following page contains interesting information on the relation of 1VAS with [Thymine Dimers]. Full crystallographic information is available from 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:8521494

Page seeded by OCA on Mon Mar 31 00:21:47 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vas"
Personal tools