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.

1i3j

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 09:11, 10 January 2018

CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE

Structural highlights

1i3j is a 3 chain structure with sequence from Bpt4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TEV1_BPT4] This endonuclease is specific to the thymidylate synthase (td) gene splice junction and is involved in intron homing.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target reveals an unusually extended structure composed of three subdomains: a Zn finger, an elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The protein wraps around the DNA, mostly following the minor groove, contacting the phosphate backbone along the full length of the duplex. Surprisingly, while the minor groove-binding helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion site. The multiple base-specific interactions over a long segment of the substrate are consistent with the observed high site specificity in spite of sequence tolerance, while the modular composition of the domain is pertinent to the evolution of homing endonucleases.

Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.,Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V EMBO J. 2001 Jul 16;20(14):3631-7. PMID:11447104^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V. Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate. EMBO J. 2001 Jul 16;20(14):3631-7. PMID:11447104 doi:10.1093/emboj/20.14.3631

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1i3j"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE==
 <StructureSection load='1i3j' size='340' side='right' caption='[[1i3j]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[1i3j]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1I3J FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1i3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3j OCA], [http://pdbe.org/1i3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i3j RCSB], [http://www.ebi.ac.uk/pdbsum/1i3j PDBsum]</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=1i3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3j OCA], [http://pdbe.org/1i3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i3j RCSB], [http://www.ebi.ac.uk/pdbsum/1i3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3j ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3j_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 27: / Line 28: @@
 </div>
 <div class="pdbe-citations 1i3j" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Endonuclease|Endonuclease]]
 == References ==
 <references/>

1i3j

From Proteopedia

Revision as of 09:11, 10 January 2018

CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox