5gkf: Difference between revisions

Latest revision as of 11:34, 2 August 2023

Structure of EndoMS-dsDNA1' complex

Structural highlights

5gkf is a 4 chain structure with sequence from Thermococcus kodakarensis KOD1 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	MG, MPD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUCS_THEKO Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.

Publication Abstract from PubMed

Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.,Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T Structure. 2016 Oct 17. pii: S0969-2126(16)30294-5. doi:, 10.1016/j.str.2016.09.005. PMID:27773688^[1]

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

References

↑ Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T. Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease. Structure. 2016 Oct 17. pii: S0969-2126(16)30294-5. doi:, 10.1016/j.str.2016.09.005. PMID:27773688 doi:https://dx.doi.org/10.1016/j.str.2016.09.005

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OCA

[1] Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T. Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease. Structure. 2016 Oct 17. pii: S0969-2126(16)30294-5. doi:, 10.1016/j.str.2016.09.005. PMID:27773688 doi:https://dx.doi.org/10.1016/j.str.2016.09.005

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5gkf' size='340' side='right'caption='[[5gkf]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gke|5gke]], [[5gkg|5gkg]], [[5gkh|5gkh]], [[5gki|5gki]], [[5gkj|5gkj]]</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1898 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5gkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkf OCA], [https://pdbe.org/5gkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gkf RCSB], [https://www.ebi.ac.uk/pdbsum/5gkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkf 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=5gkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkf OCA], [http://pdbe.org/5gkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkf RCSB], [http://www.ebi.ac.uk/pdbsum/5gkf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NUCS_THEKO NUCS_THEKO]] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.
+[https://www.uniprot.org/uniprot/NUCS_THEKO NUCS_THEKO] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Hijikata, A]]
+[[Category: Synthetic construct]]
-[[Category: Ishino, S]]
+[[Category: Thermococcus kodakarensis KOD1]]
-[[Category: Ishino, Y]]
+[[Category: Hijikata A]]
-[[Category: Kouyama, K]]
+[[Category: Ishino S]]
-[[Category: Mayanagi, K]]
+[[Category: Ishino Y]]
-[[Category: Nakae, S]]
+[[Category: Kouyama K]]
-[[Category: Shirai, T]]
+[[Category: Mayanagi K]]
-[[Category: Tsuji, T]]
+[[Category: Nakae S]]
-[[Category: Yonezawa, K]]
+[[Category: Shirai T]]
-[[Category: Dna complex]]
+[[Category: Tsuji T]]
-[[Category: Endonuclease]]
+[[Category: Yonezawa K]]
-[[Category: Hydrolase-dna complex]]

5gkf: Difference between revisions

Latest revision as of 11:34, 2 August 2023

Structure of EndoMS-dsDNA1' complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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