6ppj: Difference between revisions

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 <SX load='6ppj' size='340' side='right' viewer='molstar' caption='[[6ppj]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ppj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PPJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ppj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PPJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pcrA_2, ERS451418_01974 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889]), pcrA_1, ERS451418_01973 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</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=6ppj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppj OCA], [https://pdbe.org/6ppj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ppj RCSB], [https://www.ebi.ac.uk/pdbsum/6ppj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppj ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ppj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppj OCA], [http://pdbe.org/6ppj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppj RCSB], [http://www.ebi.ac.uk/pdbsum/6ppj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppj ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A0QTS0_MYCS2 A0QTS0_MYCS2]
-Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal motor domain and a C-terminal nuclease domain. Here we report cryoelectron microscopy (cryo-EM) structures of AdnAB in three functional states: in the absence of DNA and in complex with forked duplex DNAs before and after cleavage of the 5' single-strand DNA (ssDNA) tail by the AdnA nuclease. The structures reveal the path of the 5' ssDNA through the AdnA nuclease domain and the mechanism of 5' strand cleavage; the path of the 3' tracking strand through the AdnB motor and the DNA contacts that couple ATP hydrolysis to mechanical work; the position of the AdnA iron-sulfur cluster subdomain at the Y junction and its likely role in maintaining the split trajectories of the unwound 5' and 3' strands. Single-molecule DNA curtain analysis of DSB resection reveals that AdnAB is highly processive but prone to spontaneous pausing at random sites on duplex DNA. A striking property of AdnAB is that the velocity of DSB resection slows after the enzyme experiences a spontaneous pause. Our results highlight shared as well as distinctive properties of AdnAB vis-a-vis the RecBCD and AddAB clades of bacterial DSB-resecting motor nucleases.
-Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection.,Jia N, Unciuleac MC, Xue C, Greene EC, Patel DJ, Shuman S Proc Natl Acad Sci U S A. 2019 Nov 18. pii: 1913546116. doi:, 10.1073/pnas.1913546116. PMID:31740608<ref>PMID:31740608</ref>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6ppj" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </SX>
-[[Category: Bacillus smegmatis trevisan 1889]]
-[[Category: DNA helicase]]
 [[Category: Large Structures]]
-[[Category: Jia, N]]
+[[Category: Mycolicibacterium smegmatis]]
-[[Category: Patel, D J]]
+[[Category: Jia N]]
-[[Category: Shuman, S]]
+[[Category: Patel DJ]]
-[[Category: Unciuleac, M]]
+[[Category: Shuman S]]
-[[Category: Dna binding protein]]
+[[Category: Unciuleac M]]