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1ph5

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Revision as of 11:06, 11 September 2015

CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG(3DR)GG

Structural highlights

1ph5 is a 5 chain structure with sequence from Ciliate. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	1otc, 1jb7, 1kix, 1k8g, 1pa6, 1ph1, 1ph2, 1ph3, 1ph4, 1ph6, 1ph7, 1ph8, 1ph9, 1phj
Gene:	MAC-56A AND MAC-56K AND MAC-56S (Ciliate), MAC-41A AND MAC-41S (Ciliate)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[TEBB_OXYNO] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification. [TEBA_OXYNO] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.

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

Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.

Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.,Theobald DL, Schultz SC EMBO J. 2003 Aug 15;22(16):4314-24. PMID:12912928^[1]

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

References

↑ Theobald DL, Schultz SC. Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes. EMBO J. 2003 Aug 15;22(16):4314-24. PMID:12912928 doi:http://dx.doi.org/10.1093/emboj/cdg415

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/1ph5"

@@ Line 2: / Line 2: @@
 <StructureSection load='1ph5' size='340' side='right' caption='[[1ph5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ph5]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PH5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ph5]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ciliate Ciliate]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PH5 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1otc|1otc]], [[1jb7|1jb7]], [[1kix|1kix]], [[1k8g|1k8g]], [[1pa6|1pa6]], [[1ph1|1ph1]], [[1ph2|1ph2]], [[1ph3|1ph3]], [[1ph4|1ph4]], [[1ph6|1ph6]], [[1ph7|1ph7]], [[1ph8|1ph8]], [[1ph9|1ph9]], [[1phj|1phj]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</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=1ph5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ph5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ph5 RCSB], [http://www.ebi.ac.uk/pdbsum/1ph5 PDBsum]</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=1ph5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ph5 OCA], [http://pdbe.org/1ph5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ph5 RCSB], [http://www.ebi.ac.uk/pdbsum/1ph5 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 29: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ph5" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Sterkiella nova]]
+[[Category: Ciliate]]
 [[Category: Schultz, S C]]
 [[Category: Theobald, D L]]

1ph5

From Proteopedia

Revision as of 11:06, 11 September 2015

CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG(3DR)GG

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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