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New page: left|200px<br /><applet load="2pvi" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pvi, resolution 1.76Å" /> '''PVUII ENDONUCLEASE C...
 
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[[Image:2pvi.gif|left|200px]]<br /><applet load="2pvi" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2pvi, resolution 1.76&Aring;" />
'''PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA'''<br />


==Overview==
==PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA==
In restriction-modification systems, cleavage of substrate sites in, cellular DNA by the restriction endonuclease is prevented by the action of, a cognate methyltransferase that acts on the same substrate sites. The, PvuII restriction endonuclease (R.PvuII) has been structurally, characterized in a complex with substrate DNA (Cheng et al., 1994) and as, an apoenzyme (Athanasiadis et al., 1994). We report here a structure, determined to 1.9 A resolution by crystallography, of a complex between, R.PvuII and iodinated DNA. The presence of an iodine at the 5-carbon of, the methylatable cytosine results in the following changes in the protein:, His84 moved away from the modified base; this movement was amplified in, His85 and disrupts an intersubunit hydrogen bond; and the base, modification disturbs the distribution of water molecules that associate, with these histidine residues and the area of the scissile bond., Considering these observations, hypotheses are given as to why a similar, oligonucleotide, where a methyl group resides on the 5-carbon of the, methylatable cytosine, is slowly cleaved by R.PvuII (Rice et al., 1995).
<StructureSection load='2pvi' size='340' side='right'caption='[[2pvi]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2pvi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PVI FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C38:5-IODO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C38</scene></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=2pvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pvi OCA], [https://pdbe.org/2pvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pvi RCSB], [https://www.ebi.ac.uk/pdbsum/2pvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pvi ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/T2P2_PROHU T2P2_PROHU] Recognizes the double-stranded sequence CAGCTG and cleaves after G-3.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In restriction-modification systems, cleavage of substrate sites in cellular DNA by the restriction endonuclease is prevented by the action of a cognate methyltransferase that acts on the same substrate sites. The PvuII restriction endonuclease (R.PvuII) has been structurally characterized in a complex with substrate DNA (Cheng et al., 1994) and as an apoenzyme (Athanasiadis et al., 1994). We report here a structure, determined to 1.9 A resolution by crystallography, of a complex between R.PvuII and iodinated DNA. The presence of an iodine at the 5-carbon of the methylatable cytosine results in the following changes in the protein: His84 moved away from the modified base; this movement was amplified in His85 and disrupts an intersubunit hydrogen bond; and the base modification disturbs the distribution of water molecules that associate with these histidine residues and the area of the scissile bond. Considering these observations, hypotheses are given as to why a similar oligonucleotide, where a methyl group resides on the 5-carbon of the methylatable cytosine, is slowly cleaved by R.PvuII (Rice et al., 1995).


==About this Structure==
How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?,Horton JR, Bonventre J, Cheng X Biol Chem. 1998 Apr-May;379(4-5):451-8. PMID:9628337<ref>PMID:9628337</ref>
2PVI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Active as [http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PVI OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?, Horton JR, Bonventre J, Cheng X, Biol Chem. 1998 Apr-May;379(4-5):451-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9628337 9628337]
</div>
<div class="pdbe-citations 2pvi" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Proteus vulgaris]]
[[Category: Proteus vulgaris]]
[[Category: Single protein]]
[[Category: Cheng X]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Horton J]]
[[Category: Cheng, X.]]
[[Category: Horton, J.]]
[[Category: complex (restriction endonuclease/dna)]]
 
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Latest revision as of 07:16, 9 August 2023

PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA

2pvi, resolution 1.76Å

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