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7n8k

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LINE-1 endonuclease domain complex with Mg

Structural highlights

7n8k is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.01Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LORF2_HUMAN Has a reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Has also an endonuclease activity that allows the introduction of nicks in the chromosomal target DNA. Cleaves DNA in AT-rich regions between a 5' stretch of purines and a 3' stretch of pyrimidines, corresponding to sites of LINE-1 integration in the genome.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising approximately 20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1's ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5'-TTTTT/AA-3'. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN's sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes 'compression' near the cleavage site. This provides multiple advantages for L1-EN's role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.,Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S Nucleic Acids Res. 2021 Sep 23. pii: 6374484. doi: 10.1093/nar/gkab826. PMID:34554261^[4]

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

References

↑ Dombroski BA, Feng Q, Mathias SL, Sassaman DM, Scott AF, Kazazian HH Jr, Boeke JD. An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol Cell Biol. 1994 Jul;14(7):4485-92. doi: 10.1128/mcb.14.7.4485-4492.1994. PMID:7516468 doi:http://dx.doi.org/10.1128/mcb.14.7.4485-4492.1994
↑ Feng Q, Moran JV, Kazazian HH Jr, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 1996 Nov 29;87(5):905-16. doi: 10.1016/s0092-8674(00)81997-2. PMID:8945517 doi:http://dx.doi.org/10.1016/s0092-8674(00)81997-2
↑ Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, Gabriel A, Swergold GD, Kazazian HH Jr. Many human L1 elements are capable of retrotransposition. Nat Genet. 1997 May;16(1):37-43. PMID:9140393 doi:http://dx.doi.org/10.1038/ng0597-37
↑ Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S. Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res. 2021 Sep 23. pii: 6374484. doi: 10.1093/nar/gkab826. PMID:34554261 doi:http://dx.doi.org/10.1093/nar/gkab826

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7n8k"

Categories: Homo sapiens | Large Structures | Korolev S | Miller I

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7n8k is ON HOLD
+==LINE-1 endonuclease domain complex with Mg==
+<StructureSection load='7n8k' size='340' side='right'caption='[[7n8k]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7n8k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N8K 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]] 2.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=7n8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n8k OCA], [https://pdbe.org/7n8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n8k RCSB], [https://www.ebi.ac.uk/pdbsum/7n8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n8k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LORF2_HUMAN LORF2_HUMAN] Has a reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Has also an endonuclease activity that allows the introduction of nicks in the chromosomal target DNA. Cleaves DNA in AT-rich regions between a 5' stretch of purines and a 3' stretch of pyrimidines, corresponding to sites of LINE-1 integration in the genome.<ref>PMID:7516468</ref> <ref>PMID:8945517</ref> <ref>PMID:9140393</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising approximately 20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1's ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5'-TTTTT/AA-3'. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN's sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes 'compression' near the cleavage site. This provides multiple advantages for L1-EN's role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.
-Authors: Korolev, S., Miller, I.
+Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.,Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S Nucleic Acids Res. 2021 Sep 23. pii: 6374484. doi: 10.1093/nar/gkab826. PMID:34554261<ref>PMID:34554261</ref>
-Description: LINE-1 endonuclease domain complex with Mg
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Korolev, S]]
+<div class="pdbe-citations 7n8k" style="background-color:#fffaf0;"></div>
-[[Category: Miller, I]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Korolev S]]
+[[Category: Miller I]]

7n8k

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Current revision

LINE-1 endonuclease domain complex with Mg

Structural highlights

Function

Publication Abstract from PubMed

References

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