1phj: Difference between revisions

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<StructureSection load='1phj' size='340' side='right'caption='[[1phj]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1phj' size='340' side='right'caption='[[1phj]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1phj]] 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=1PHJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PHJ FirstGlance]. <br>
<table><tr><td colspan='2'>[[1phj]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PHJ FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#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;'>[[1otc|1otc]], [[1jb7|1jb7]], [[1kix|1kix]], [[1k8g|1k8g]], [[1pa6|1pa6]], [[1ph1|1ph1]], [[1ph2|1ph2]], [[1ph3|1ph3]], [[1ph4|1ph4]], [[1ph5|1ph5]], [[1ph6|1ph6]], [[1ph7|1ph7]], [[1ph8|1ph8]], [[1ph9|1ph9]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1phj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1phj OCA], [https://pdbe.org/1phj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1phj RCSB], [https://www.ebi.ac.uk/pdbsum/1phj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1phj 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=1phj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1phj OCA], [http://pdbe.org/1phj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1phj RCSB], [http://www.ebi.ac.uk/pdbsum/1phj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1phj ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/TEBB_OXYNO 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. [[http://www.uniprot.org/uniprot/TEBA_OXYNO 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.  
[https://www.uniprot.org/uniprot/TEBA_STENO TEBA_STENO] 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1phj ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1phj ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:12912928</ref>
==See Also==
 
*[[End-binding protein|End-binding protein]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1phj" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ciliate]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Schultz, S C]]
[[Category: Sterkiella nova]]
[[Category: Theobald, D L]]
[[Category: Schultz SC]]
[[Category: Dna binding protein-dna complex]]
[[Category: Theobald DL]]
[[Category: Noncognate]]
[[Category: Ob fold]]
[[Category: Oligonucleotide and oligosaccharide binding fold]]
[[Category: Protein dna interaction]]
[[Category: Protein/dna]]
[[Category: Sequence specificity]]
[[Category: Single strand dna binding protein]]
[[Category: Telomere]]

Latest revision as of 11:08, 14 February 2024

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

Structural highlights

1phj is a 5 chain structure with sequence from Sterkiella nova. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TEBA_STENO 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.

See Also

1phj, resolution 2.50Å

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