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3hqg

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Revision as of 07:58, 12 December 2018

Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA

Structural highlights

3hqg is a 3 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1na6, 3hqf
Gene:	ECORII, ecoRIIR ("Bacillus coli" Migula 1895)
Activity:	Type II site-specific deoxyribonuclease, with EC number 3.1.21.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[T2E2_ECOLX] Recognizes the double-stranded sequence CCWGG and cleaves before C-1.

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

EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.

Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.,Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V Nucleic Acids Res. 2009 Oct;37(19):6613-24. Epub 2009 Sep 3. PMID:19729506^[1]

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

References

↑ Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V. Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res. 2009 Oct;37(19):6613-24. Epub 2009 Sep 3. PMID:19729506 doi:10.1093/nar/gkp699

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hqg"

@@ Line 1: / Line 1: @@
 ==Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA==
 <StructureSection load='3hqg' size='340' side='right' caption='[[3hqg]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECORII, ecoRIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=3hqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hqg OCA], [http://pdbe.org/3hqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hqg RCSB], [http://www.ebi.ac.uk/pdbsum/3hqg 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=3hqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hqg OCA], [http://pdbe.org/3hqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hqg RCSB], [http://www.ebi.ac.uk/pdbsum/3hqg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hqg ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hq/3hqg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hq/3hqg_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

3hqg

From Proteopedia

Revision as of 07:58, 12 December 2018

Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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