This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1vyb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Endonuclease domain of human LINE1 ORF2p

Structural highlights

1vyb 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 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 L1 endonuclease (L1-EN) is encoded by the non-LTR retrotransposon LINE-1 (L1). L1 is responsible for more than 1.5 million retrotransposition events in the history of the human genome, contributing more than a quarter to human genomic DNA (L1 and Alu elements). L1-EN is related to the well-understood human DNA repair endonuclease APE1, and its nicking specificity is a major determinant for retrotransposon integration site selection. The crystal structure of human L1 endonuclease is the first of a retrotransposon-encoded protein and a prototype for retrotransposon-encoded endonucleases involved in target-primed reverse transcription. Structure-based endonuclease alignments reveal a conserved threonine in addition to previously identified invariant residues and suggest that DNA recognition proceeds via the accommodation of an extrahelical nucleotide within a pocket of the enzyme. The present analysis will help to refine phylogenetic and functional relationships among metal-dependent phosphohydrolases and provides a basis for manipulating non-LTR retrotransposon integration site selection.

Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.,Weichenrieder O, Repanas K, Perrakis A Structure. 2004 Jun;12(6):975-86. PMID:15274918^[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
↑ Weichenrieder O, Repanas K, Perrakis A. Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon. Structure. 2004 Jun;12(6):975-86. PMID:15274918 doi:10.1016/j.str.2004.04.011

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/1vyb"

Categories: Homo sapiens | Large Structures | Perrakis A | Repanas K | Weichenrieder O

@@ Line 3: / Line 3: @@
 <StructureSection load='1vyb' size='340' side='right'caption='[[1vyb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vyb]] is a 2 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=1VYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VYB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vyb]] 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=1VYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VYB 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=SO3:SULFITE+ION'>SO3</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</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=1vyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vyb OCA], [https://pdbe.org/1vyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vyb RCSB], [https://www.ebi.ac.uk/pdbsum/1vyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vyb 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 30: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Perrakis, A]]
+[[Category: Perrakis A]]
-[[Category: Repanas, K]]
+[[Category: Repanas K]]
-[[Category: Weichenrieder, O]]
+[[Category: Weichenrieder O]]
-[[Category: Ape-1 type]]
-[[Category: Endonuclease]]
-[[Category: Retrotransposition]]
-[[Category: Retrotransposon]]
-[[Category: Rna-directed dna polymerase]]
-[[Category: Transferase]]

1vyb

From Proteopedia

Current revision

Endonuclease domain of human LINE1 ORF2p

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox