6f1s: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==C-terminal domain of CglI restriction endonuclease H subunit==
-<StructureSection load='6f1s' size='340' side='right' caption='[[6f1s]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='6f1s' size='340' side='right'caption='[[6f1s]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6f1s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F1S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6f1s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F1S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 2.4&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cglIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1718 "Micrococcus glutamicus" Kinoshita et al. 1958])</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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [https://pdbe.org/6f1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [https://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s 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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [http://pdbe.org/6f1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [http://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/H7C664_CORGT H7C664_CORGT]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has unusual Walker A and Motif VI sequences those nonetheless have their expected functions. Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163-aa 172), that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a dimeric complex.
+The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.,Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M Nucleic Acids Res. 2018 Feb 20. pii: 4877023. doi: 10.1093/nar/gky107. PMID:29471489<ref>PMID:29471489</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6f1s" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Micrococcus glutamicus kinoshita et al. 1958]]
+[[Category: Corynebacterium glutamicum]]
-[[Category: Grigaitis, R]]
+[[Category: Large Structures]]
-[[Category: Silanskas, A]]
+[[Category: Grigaitis R]]
-[[Category: Tamulaitiene, G]]
+[[Category: Silanskas A]]
-[[Category: Zaremba, M]]
+[[Category: Tamulaitiene G]]
-[[Category: Hydrolase]]
+[[Category: Zaremba M]]
-[[Category: Ntpase]]
-[[Category: Restriction endonuclease]]