1l2m

From Proteopedia

(Difference between revisions)

Revision as of 07:54, 25 November 2020

Minimized Average Structure of the N-terminal, DNA-binding domain of the replication initiation protein from a geminivirus (Tomato yellow leaf curl virus-Sardinia)

Structural highlights

1l2m is a 1 chain structure with sequence from Tycsv. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1l5i
Gene:	rep (TYCSV)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[REP_TYCSV] Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific region at the genome origin of replication. It introduces an endonucleolytic nick within the conserved sequence 5'-TAATATTAC-3' in the intergenic region of the genome present in all geminiviruses, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities.

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

Rolling circle replication is a mechanism for copying single-stranded genomes by means of double-stranded intermediates. A multifunctional replication initiator protein (Rep) is indispensable for the precise initiation and termination of this process. Despite the ubiquitous presence and fundamental importance of rolling circle replication elements, structural information on their respective replication initiators is still missing. Here we present the solution NMR structure of the catalytic domain of Rep, the initiator protein of tomato yellow leaf curl virus. It is composed of a central five-stranded anti-parallel beta-sheet, flanked by a small two-stranded beta-sheet, a beta-hairpin and two alpha-helices. Surprisingly, the structure reveals that the catalytic Rep domain is related to a large group of proteins that bind RNA or DNA. Identification of Rep as resembling the family of ribonucleoprotein/RNA-recognition motif fold proteins establishes a structure-based evolutionary link between RNA binding proteins, splicing factors, and replication initiators of prokaryotic and eukaryotic single-stranded DNA elements and mammalian DNA tumor viruses.

The structure of a replication initiator unites diverse aspects of nucleic acid metabolism.,Campos-Olivas R, Louis JM, Clerot D, Gronenborn B, Gronenborn AM Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10310-5. Epub 2002 Jul 18. PMID:12130667^[1]

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

References

↑ Campos-Olivas R, Louis JM, Clerot D, Gronenborn B, Gronenborn AM. The structure of a replication initiator unites diverse aspects of nucleic acid metabolism. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10310-5. Epub 2002 Jul 18. PMID:12130667 doi:10.1073/pnas.152342699

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/1l2m"

@@ Line 1: / Line 1: @@
 ==Minimized Average Structure of the N-terminal, DNA-binding domain of the replication initiation protein from a geminivirus (Tomato yellow leaf curl virus-Sardinia)==
-<StructureSection load='1l2m' size='340' side='right' caption='[[1l2m]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1l2m' size='340' side='right'caption='[[1l2m]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1l2m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Tycsv Tycsv]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L2M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1l2m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Tycsv Tycsv]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L2M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L2M FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1l5i|1l5i]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l5i|1l5i]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rep ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=123735 TYCSV])</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=1l2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l2m OCA], [http://pdbe.org/1l2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l2m RCSB], [http://www.ebi.ac.uk/pdbsum/1l2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l2m ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1l2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l2m OCA], [http://pdbe.org/1l2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l2m RCSB], [http://www.ebi.ac.uk/pdbsum/1l2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l2m ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Tycsv]]
 [[Category: Campos-Olivas, R]]

1l2m

From Proteopedia

Revision as of 07:54, 25 November 2020

Minimized Average Structure of the N-terminal, DNA-binding domain of the replication initiation protein from a geminivirus (Tomato yellow leaf curl virus-Sardinia)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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