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.


3ldy

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:46, 7 February 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI==
==An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI==
-
<StructureSection load='3ldy' size='340' side='right' caption='[[3ldy]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+
<StructureSection load='3ldy' size='340' side='right'caption='[[3ldy]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ldy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14909 Atcc 14909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LDY FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ldy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_alcaligenes Pseudomonas alcaligenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LDY FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 1.97&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3m7k|3m7k]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pacIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=43263 ATCC 14909])</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=3ldy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldy OCA], [https://pdbe.org/3ldy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ldy RCSB], [https://www.ebi.ac.uk/pdbsum/3ldy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ldy ProSAT]</span></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=3ldy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldy OCA], [http://pdbe.org/3ldy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ldy RCSB], [http://www.ebi.ac.uk/pdbsum/3ldy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ldy ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/D5MNX7_PSEAC D5MNX7_PSEAC]
-
The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 A resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA base pairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures.
+
-
 
+
-
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.,Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan RD, Wilson GG, Stoddard BL Structure. 2010 Jun 9;18(6):734-43. PMID:20541511<ref>PMID:20541511</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3ldy" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Endonuclease|Endonuclease]]
+
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 14909]]
+
[[Category: Large Structures]]
-
[[Category: Chan, S H]]
+
[[Category: Pseudomonas alcaligenes]]
-
[[Category: Heiter, D]]
+
[[Category: Chan S-H]]
-
[[Category: Shen, B W]]
+
[[Category: Heiter D]]
-
[[Category: Stoddard, B L]]
+
[[Category: Shen BW]]
-
[[Category: Wilson, G]]
+
[[Category: Stoddard BL]]
-
[[Category: Xu, S Y]]
+
[[Category: Wilson G]]
-
[[Category: A-a]]
+
[[Category: Xu S-Y]]
-
[[Category: And t-t base-pair]]
+
-
[[Category: Beta-beta-alpha-metal]]
+
-
[[Category: Hnh motif]]
+
-
[[Category: Hydrolase-dna complex]]
+
-
[[Category: Zinc cluster]]
+

Current revision

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

PDB ID 3ldy

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ldy"
Personal tools