View source for 3wvk


==Time-Resolved Crystal Structure of HindIII with 230sec soaking==
<StructureSection load='3wvk' size='340' side='right'caption='[[3wvk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3wvk]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WVK 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]] 2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3wvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wvk OCA], [https://pdbe.org/3wvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wvk RCSB], [https://www.ebi.ac.uk/pdbsum/3wvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wvk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/T2D3_HAEIN T2D3_HAEIN] Recognizes the double-stranded sequence AAGCTT and cleaves after A-1.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In order to investigate the mechanism of the reaction catalyzed by HindIII, structures of HindIII-DNA complexes with varying durations of soaking time in cryoprotectant buffer containing manganese ions were determined by the freeze-trap method. In the crystal structures of the complexes obtained after soaking for a longer duration, two manganese ions, indicated by relatively higher electron density, are clearly observed at the two metal ion-binding sites in the active site of HindIII. The increase in the electron density of the two metal-ion peaks followed distinct pathways with increasing soaking times, suggesting variation in the binding rate constant for the two metal sites. DNA cleavage is observed when the second manganese ion appears, suggesting that HindIII uses the two-metal-ion mechanism, or alternatively that its reactivity is enhanced by the binding of the second metal ion. In addition, conformational change in a loop near the active site accompanies the catalytic reaction.

Analysis of the HindIII-catalyzed reaction by time-resolved crystallography.,Kawamura T, Kobayashi T, Watanabe N Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):256-65. doi:, 10.1107/S1399004714025188. Epub 2015 Jan 23. PMID:25664735<ref>PMID:25664735</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3wvk" style="background-color:#fffaf0;"></div>

==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Haemophilus influenzae Rd KW20]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Kawamura T]]
[[Category: Kobayashi T]]
[[Category: Watanabe N]]