1h56: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
Line 1: Line 1:
[[Image:1h56.png|left|200px]]
==STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A NEW MAGNESIUM ION BINDING SITE NEAR TYR94 IN THE RESTRICTION ENDONUCLEASE PVUII==
<StructureSection load='1h56' size='340' side='right' caption='[[1h56]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1h56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H56 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1eyu|1eyu]], [[1f0o|1f0o]], [[1k0z|1k0z]], [[1ni0|1ni0]], [[1pvi|1pvi]], [[1pvu|1pvu]], [[2pvi|2pvi]], [[3pvi|3pvi]]</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1h56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h56 RCSB], [http://www.ebi.ac.uk/pdbsum/1h56 PDBsum]</span></td></tr>
<table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+). According to the structural data, divalent metal ion binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+) complex has two distinct metal ion binding sites, one in each monomer. One site is formed by the catalytic residues Asp58 and Glu68, and has extensive similarities to a catalytically important site found in all structurally examined restriction endonucleases. The other binding site is located in the other monomer, in the immediate vicinity of the hydroxyl group of Tyr94; it has no analogy to metal ion binding sites found so far in restriction endonucleases. To assign the number of metal ions involved and to better understand the role of Mg(2+) binding to Tyr94 for the function of PvuII, we have exchanged Tyr94 by Phe and characterized the metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F variant. Wild-type PvuII cleaves both strands of the DNA in a concerted reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA cleavage, occurs with a Hill coefficient of 4, meaning that at least two metal ions are bound to each subunit in a cooperative fashion upon formation of the active complex. Quenched-flow experiments show that DNA cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with enzyme or DNA than if preformed enzyme-DNA complexes are mixed with Mg(2+). These results show that Mg(2+) cannot easily enter the active center of the preformed enzyme-DNA complex, but that for fast cleavage the metal ions must already be bound to the apoenzyme and carried with the enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to wild-type PvuII, does not cleave DNA in a concerted manner and metal ion binding occurs with a Hill coefficient of 1. These results indicate that removal of the Mg(2+) binding site at Tyr94 completely disrupts the cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F cleaves DNA about ten times more slowly than wild-type PvuII, regardless of the order of mixing. From these results we conclude that wild-type PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+) required for catalysis are already bound at the enzyme, one of them at Tyr94. We suggest that this Mg(2+) is shifted to the active center during binding of a specific DNA substrate. These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter the catalytic center of restriction endonucleases.


{{STRUCTURE_1h56|  PDB=1h56  |  SCENE=  }}
Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII.,Spyridaki A, Matzen C, Lanio T, Jeltsch A, Simoncsits A, Athanasiadis A, Scheuring-Vanamee E, Kokkinidis M, Pingoud A J Mol Biol. 2003 Aug 8;331(2):395-406. PMID:12888347<ref>PMID:12888347</ref>


===STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A NEW MAGNESIUM ION BINDING SITE NEAR TYR94 IN THE RESTRICTION ENDONUCLEASE PVUII===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_12888347}}
 
==About this Structure==
[[1h56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H56 OCA].


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease|Endonuclease]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:012888347</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Proteus vulgaris]]
[[Category: Proteus vulgaris]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Type II site-specific deoxyribonuclease]]
Retrieved from "https://proteopedia.org/1h56"