2w00

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (05:33, 17 October 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2w00.png|left|200px]]
 
-
<!--
+
==Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP==
-
The line below this paragraph, containing "STRUCTURE_2w00", creates the "Structure Box" on the page.
+
<StructureSection load='2w00' size='340' side='right'caption='[[2w00]], [[Resolution|resolution]] 2.60&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'>[[2w00]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W00 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]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
{{STRUCTURE_2w00| PDB=2w00 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w00 OCA], [https://pdbe.org/2w00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w00 RCSB], [https://www.ebi.ac.uk/pdbsum/2w00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w00 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/T1R1_ECOLX T1R1_ECOLX] The restriction (R) subunit of a type I restriction enzyme that recognizes 5'-GAAN(6)RTCG-3' (for EcoR124I) and 5'-GAAN(7)RTCG-3' (for EcoR124II) and cleaves a random distance away (PubMed:2784505). Subunit R is required for both nuclease and ATPase activities, but not for modification (Probable) (PubMed:12654995). After locating an unmethylated recognition site, the enzyme complex serves as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage (PubMed:15300241). The enzyme undergoes major structural changes to bring the motor domains into contact with DNA, allowing DNA translocation. This prevents DNA access to the catalytic domains of both the R and M subunits, preventing both restriction and methylation (PubMed:32483229). The R(1)M(2)S(1) complex translocates an average of 555 bp/second on nicked DNA; the R(2)M(2)S(1) complex translocates at double that speed (PubMed:15300241). The 2 R subunit motors are independent and track along the helical pitch of the DNA, inducing positive supercoiling ahead of themselves (PubMed:15300241).<ref>PMID:15300241</ref> <ref>PMID:2784505</ref> <ref>PMID:32483229</ref> <ref>PMID:12654995</ref> <ref>PMID:32483229</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/w0/2w00_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2w00 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Type I restriction-modification enzymes act as conventional adenine methylases on hemimethylated DNAs, but unmethylated recognition targets induce them to translocate thousands of base pairs before cleaving distant sites nonspecifically. The first crystal structure of a type I motor subunit responsible for translocation and cleavage suggests how the pentameric translocating complex is assembled and provides a structural framework for translocation of duplex DNA by RecA-like ATPase motors.
-
===CRYSTAL STRUCTURE OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP===
+
Structure of the motor subunit of type I restriction-modification complex EcoR124I.,Lapkouski M, Panjikar S, Janscak P, Smatanova IK, Carey J, Ettrich R, Csefalvay E Nat Struct Mol Biol. 2008 Dec 14. PMID:19079266<ref>PMID:19079266</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19079266}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2w00" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19079266 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_19079266}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2W00 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W00 OCA].
+
-
 
+
-
==Reference==
+
-
Structure of the motor subunit of type I restriction-modification complex EcoR124I., Lapkouski M, Panjikar S, Janscak P, Smatanova IK, Carey J, Ettrich R, Csefalvay E, Nat Struct Mol Biol. 2008 Dec 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19079266 19079266]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Type I site-specific deoxyribonuclease]]
+
[[Category: Csefalvay E]]
-
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+
[[Category: Ettrich R]]
-
[[Category: Atp-binding]]
+
[[Category: Kuta Smatanova I]]
-
[[Category: Dna-binding]]
+
[[Category: Lapkouski M]]
-
[[Category: Helicase]]
+
[[Category: Panjikar S]]
-
[[Category: Hydrolase]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Plasmid]]
+
-
[[Category: R ecor124i]]
+
-
[[Category: Restriction system]]
+
-
[[Category: Type i restriction-modification enzyme]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:12:14 2009''
+

Current revision

Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP

PDB ID 2w00

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/2w00"
Personal tools