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==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==
==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==
<StructureSection load='2end' size='340' side='right' caption='[[2end]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='2end' size='340' side='right'caption='[[2end]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2end]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1end 1end]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2END OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2END FirstGlance]. <br>
<table><tr><td colspan='2'>[[2end]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1end 1end]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2END OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2END FirstGlance]. <br>
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></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]] 1.45&#8491;</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=2end FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2end OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2end RCSB], [http://www.ebi.ac.uk/pdbsum/2end PDBsum]</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=2end FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2end OCA], [https://pdbe.org/2end PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2end RCSB], [https://www.ebi.ac.uk/pdbsum/2end PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2end 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]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/2end_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/2end_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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=2end ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystallographic study of bacteriophage T4 endonuclease V, which is involved in the initial step of the pyrimidine dimer-specific excision repair pathway, has been carried out with respect to the wild-type and three different mutant enzymes. This enzyme catalyzes the cleavage of the N-glycosyl bond at the 5'-side of the pyrimidine dimer, and subsequently incises the phosphodiester bond at the apyrimidinic site through a beta-elimination reaction. The structure of the wild-type enzyme refined at 1.45 A resolution reveals the detailed molecular architecture. The enzyme is composed of a single compact domain classified as an all-alpha structure. The molecule is stabilized mainly by three hydrophobic cores, two of which include many aromatic side-chain interactions. The structure has a unique folding motif, where the amino-terminal segment penetrates between two major alpha-helices and prevents their direct contact, and it is incompatible with the close-packing category of helices for protein folding. The concave surface, covered with many positive charges, implies an interface for DNA binding. The glycosylase catalytic center, which comprises Glu23 and the surrounding basic residues Arg3, Arg22 and Arg26, lie in this basic surface. The crystal structures of the three active-site mutants, in which Glu23 was replaced by Gln(E23Q) and Asp (E23D), respectively, and Arg3 by Gln (R3Q), have been determined at atomic resolution. The backbone structures of the E23Q and R3Q mutants were almost identical with that of the wild-type, while the E23D mutation induces a small, but significant, change in the backbone structure, such as an increase of the central kink of the H1 helix at Pro25. In the catalytic center of the glycosylase, however, these three mutations do not generate notable movements of protein atoms, except for significant shifts of some bound water molecules. Thus, the structural differences between the wild-type and each mutant are confined to the remarkably small region around their replaced chemical groups. Combined with the biochemical studies and the difference circular dichroism measurements, these results allow us to conclude that the negatively charged carboxyl group of Glu23 is essential for the cleavage of the N-glycosyl bond, and that the positively charged guanidino group of Arg3 is crucial to bind the substrate, a DNA duplex containing a pyrimidine dimer. The amino terminal alpha-amino group is located at a position approximately 4.4 A away from the carboxyl group of Glu23. These structural features are generally consistent with the reaction scheme proposed by Dodson and co-workers.
Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.,Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E J Mol Biol. 1995 Jun 2;249(2):360-75. PMID:7783199<ref>PMID:7783199</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Enterobacteria phage t4]]
[[Category: Escherichia virus T4]]
[[Category: Ariyoshi, M]]
[[Category: Large Structures]]
[[Category: Katayanagi, K]]
[[Category: Ariyoshi M]]
[[Category: Matsumoto, O]]
[[Category: Katayanagi K]]
[[Category: Morikawa, K]]
[[Category: Matsumoto O]]
[[Category: Ohtsuka, E]]
[[Category: Morikawa K]]
[[Category: Vassylyev, D G]]
[[Category: Ohtsuka E]]
[[Category: Endonuclease]]
[[Category: Vassylyev DG]]

Latest revision as of 12:19, 14 February 2024

CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTSCRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS

Structural highlights

2end is a 1 chain structure with sequence from Escherichia virus T4. This structure supersedes the now removed PDB entry 1end. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.45Å
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

2end, resolution 1.45Å

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