1ir6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (23:35, 27 December 2023) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1ir6.png|left|200px]]
 
-
<!--
+
==Crystal structure of exonuclease RecJ bound to manganese==
-
The line below this paragraph, containing "STRUCTURE_1ir6", creates the "Structure Box" on the page.
+
<StructureSection load='1ir6' size='340' side='right'caption='[[1ir6]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1ir6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IR6 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
{{STRUCTURE_1ir6| PDB=1ir6 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ir6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ir6 OCA], [https://pdbe.org/1ir6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ir6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ir6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ir6 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ir6 TOPSAN]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RECJ_THET8 RECJ_THET8] Single-stranded-DNA-specific exonuclease acting in a 5' to 3' direction; has no detectable activity on ssRNA.<ref>PMID:21087930</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ir/1ir6_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ir6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
RecJ, a 5' to 3' exonuclease specific for single-stranded DNA, functions in DNA repair and recombination systems. We determined the crystal structure of RecJ bound to Mn(2+) ion essential for its activity. RecJ has a novel fold in which two domains are interconnected by a long helix, forming a central groove. Mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes RecJ proteins. The groove is composed of residues conserved among RecJ proteins and is positively charged. These findings and the narrow width of the groove indicate that the groove binds single- instead of double-stranded DNA.
-
===Crystal structure of exonuclease RecJ bound to manganese===
+
The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.,Yamagata A, Kakuta Y, Masui R, Fukuyama K Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5908-12. Epub 2002 Apr 23. PMID:11972066<ref>PMID:11972066</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1ir6" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11972066}}, adds the Publication Abstract to the page
+
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11972066 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_11972066}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
1IR6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IR6 OCA].
+
-
 
+
-
==Reference==
+
-
The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity., Yamagata A, Kakuta Y, Masui R, Fukuyama K, Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5908-12. Epub 2002 Apr 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11972066 11972066]
+
-
[[Category: Single protein]]
+
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
-
[[Category: Fukuyama, K.]]
+
[[Category: Fukuyama K]]
-
[[Category: Kakuta, Y.]]
+
[[Category: Kakuta Y]]
-
[[Category: Masui, R.]]
+
[[Category: Masui R]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Yamagata A]]
-
[[Category: Yamagata, A.]]
+
-
[[Category: Dna recombination]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Manganese]]
+
-
[[Category: Nuclease]]
+
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Single-stranded dna]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Two domains interconnected by alpha-helix]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 13:51:12 2008''
+

Current revision

Crystal structure of exonuclease RecJ bound to manganese

PDB ID 1ir6

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/1ir6"
Personal tools