2v0s

From Proteopedia

(Difference between revisions)

Current revision

crystal structure of a hairpin exchange variant (LR1) of the targeting LINE-1 retrotransposon endonuclease

Structural highlights

2v0s is a 1 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 1.8Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The human LINE-1 endonuclease (L1-EN) is the targeting endonuclease encoded by the human LINE-1 (L1) retrotransposon. L1-EN guides the genomic integration of new L1 and Alu elements that presently account for approximately 28% of the human genome. L1-EN bears considerable technological interest, because its target selectivity may ultimately be engineered to allow the site-specific integration of DNA into defined genomic locations. Based on the crystal structure, we generated L1-EN mutants to analyze and manipulate DNA target site recognition. Crystal structures and their dynamic and functional analysis show entire loop grafts to be feasible, resulting in altered specificity, while individual point mutations do not change the nicking pattern of L1-EN. Structural parameters of the DNA target seem more important for recognition than the nucleotide sequence, and nicking profiles on DNA oligonucleotides in vitro are less well defined than the respective integration site consensus in vivo. This suggests that additional factors other than the DNA nicking specificity of L1-EN contribute to the targeted integration of non-LTR retrotransposons.

Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease.,Repanas K, Zingler N, Layer LE, Schumann GG, Perrakis A, Weichenrieder O Nucleic Acids Res. 2007;35(14):4914-26. Epub 2007 Jul 10. PMID:17626046^[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
↑ Repanas K, Zingler N, Layer LE, Schumann GG, Perrakis A, Weichenrieder O. Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease. Nucleic Acids Res. 2007;35(14):4914-26. Epub 2007 Jul 10. PMID:17626046 doi:10.1093/nar/gkm516

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v0s"

@@ Line 3: / Line 3: @@
 <StructureSection load='2v0s' size='340' side='right'caption='[[2v0s]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v0s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V0S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v0s]] is a 1 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=2V0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V0S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vyb|1vyb]], [[2v0r|2v0r]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2v0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v0s OCA], [https://pdbe.org/2v0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v0s RCSB], [https://www.ebi.ac.uk/pdbsum/2v0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v0s 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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Layer, L E]]
+[[Category: Layer LE]]
-[[Category: Perrakis, A]]
+[[Category: Perrakis A]]
-[[Category: Repanas, K]]
+[[Category: Repanas K]]
-[[Category: Schumann, G G]]
+[[Category: Schumann GG]]
-[[Category: Weichenrieder, O]]
+[[Category: Weichenrieder O]]
-[[Category: Zingler, N]]
+[[Category: Zingler N]]
-[[Category: Ape-1 type]]
-[[Category: Endonuclease]]
-[[Category: Hypothetical protein]]
-[[Category: Protein engineering]]
-[[Category: Retrotransposition]]
-[[Category: Retrotransposon]]
-[[Category: Transcription]]

2v0s

From Proteopedia

Current revision

crystal structure of a hairpin exchange variant (LR1) of the targeting LINE-1 retrotransposon endonuclease

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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