View source for 6jop


==Crystal structures of phage NrS-1 N300-dNTPs-Mg2+ complex provide molecular mechanisms for substrate specificity==
<StructureSection load='6jop' size='340' side='right'caption='[[6jop]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6jop]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nitratiruptor_phage_NrS-1 Nitratiruptor phage NrS-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JOP FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.353&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=6jop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jop OCA], [https://pdbe.org/6jop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jop RCSB], [https://www.ebi.ac.uk/pdbsum/6jop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jop ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/M5AAG8_9CAUD M5AAG8_9CAUD] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A novel DNA polymerase from the deep-sea vent phage NrS-1, was characterized as a primase-polymerase (referred to as prim-pol), which works as a self-priming DNA polymerase to synthesize de novo long DNA strands. Functional research on the NrS-1 prim-pol illustrated that the N-terminal 300 residues (referred to as N300) have de novo synthesis activity similar to that of the full-length enzyme. Just like other prim-pols, NrS-1 prim-pol was able to initiate DNA synthesis, proficiently discriminating against ribonucleotides (NTPs), exclusively using deoxynucleotides (dNTPs). However, the structural basis for this discrimination is not well understood. Here, the three kinds of crystal structures of N300-dNTPs-Mg(2+) complex were determined. These complex structures shared the identical steric architecture and hydrogen-bond interactions in the catalytic center. The results of biochemical studies indicated that R145 possibly plays an indispensable role in the primer extension. Mutagenesis and structural simulation showed that the backbone carboxyl group of Y146, as a potential sugar selector, was involved in steric clashing with the incoming 2'-OH group of NTPs. However, the mechanism of substrate discrimination probably was different from that of other prim-pols, according to the structural analyses and sequence comparison.

Crystal structures of phage NrS-1 N300-dNTPs-Mg(2+) complex provide molecular mechanisms for substrate specificity.,Guo H, Li M, Wu H, Wang W, Yu F, He J Biochem Biophys Res Commun. 2019 Jun 5. pii: S0006-291X(19)31060-5. doi:, 10.1016/j.bbrc.2019.05.162. PMID:31176489<ref>PMID:31176489</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6jop" style="background-color:#fffaf0;"></div>

==See Also==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Nitratiruptor phage NrS-1]]
[[Category: Guo HJ]]
[[Category: He JH]]
[[Category: Li MJ]]
[[Category: Wu H]]
[[Category: Yu F]]