3lfu: Difference between revisions

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 <StructureSection load='3lfu' size='340' side='right'caption='[[3lfu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lfu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LFU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lfu]] is a 1 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=3LFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LFU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3813, JW3786, mutU, pdeB, rad, recL, uvrD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3lfu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lfu OCA], [https://pdbe.org/3lfu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lfu RCSB], [https://www.ebi.ac.uk/pdbsum/3lfu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lfu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/UVRD_ECOLI UVRD_ECOLI]] Has both ATPase and helicase activities. Unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present. Involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair.
+[https://www.uniprot.org/uniprot/UVRD_ECOLI UVRD_ECOLI] Has both ATPase and helicase activities. Unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present. Involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Escherichia coli UvrD is a superfamily 1 DNA helicase and single-stranded DNA (ssDNA) translocase that functions in DNA repair and plasmid replication and as an anti-recombinase by removing RecA protein from ssDNA. UvrD couples ATP binding and hydrolysis to unwind double-stranded DNA and translocate along ssDNA with 3'-to-5' directionality. Although a UvrD monomer is able to translocate along ssDNA rapidly and processively, DNA helicase activity in vitro requires a minimum of a UvrD dimer. Previous crystal structures of UvrD bound to a single-stranded DNA/duplex DNA junction show that its 2B sub-domain exists in a "closed" state and interacts with the duplex DNA. Here, we report a crystal structure of an apo form of UvrD in which the 2B sub-domain is in an "open" state that differs by an approximately 160 degrees rotation of the 2B sub-domain. To study the rotational conformational states of the 2B sub-domain in various ligation states, we constructed a series of double-cysteine UvrD mutants and labeled them with fluorophores such that rotation of the 2B sub-domain results in changes in fluorescence resonance energy transfer. These studies show that the open and closed forms can interconvert in solution, with low salt favoring the closed conformation and high salt favoring the open conformation in the absence of DNA. Binding of UvrD to DNA and ATP binding and hydrolysis also affect the rotational conformational state of the 2B sub-domain, suggesting that 2B sub-domain rotation is coupled to the function of this nucleic acid motor enzyme.
-Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA Binding.,Jia H, Korolev S, Niedziela-Majka A, Maluf NK, Gauss GH, Myong S, Ha T, Waksman G, Lohman TM J Mol Biol. 2011 Jun 17. PMID:21704638<ref>PMID:21704638</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3lfu" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Helicase 3D structures|Helicase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Korolev, S]]
+[[Category: Korolev S]]
-[[Category: Lohman, T M]]
+[[Category: Lohman TM]]
-[[Category: Waksman, G]]
+[[Category: Waksman G]]
-[[Category: Atp-binding]]
-[[Category: Dna damage]]
-[[Category: Dna helicase]]
-[[Category: Dna repair]]
-[[Category: Dna replication]]
-[[Category: Dna-binding]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Nucleotide-binding]]
-[[Category: Sf1 helicase]]
-[[Category: Sos response]]