1ph6: Difference between revisions

← Older edit Newer edit →

Revision as of 22:59, 30 March 2008

File:1ph6.gif

, resolution 2.10Å

Ligands:

, ,

Gene:

MAC-56A AND MAC-56K AND MAC-56S (Sterkiella nova), MAC-41A AND MAC-41S (Sterkiella nova)

Related:

1otc, 1jb7, 1kix, 1k8g, 1pa6, 1ph1, 1ph2, 1ph3, 1ph4, 1ph5, 1ph7, 1ph8, 1ph9, 1phj

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Crystal Structure of THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG

OverviewOverview

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.

About this StructureAbout this Structure

1PH6 is a Protein complex structure of sequences from Sterkiella nova. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Sun Mar 30 22:59:38 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 4: / Line 4: @@
 |PDB= 1ph6 |SIZE=350|CAPTION= <scene name='initialview01'>1ph6</scene>, resolution 2.10&Aring;
 |SITE=
-|LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
+|LIGAND= <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
 |ACTIVITY=
 |GENE= 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])
+|DOMAIN=
+|RELATEDENTRY=[[1otc|1otc]], [[1jb7|1jb7]], [[1kix|1kix]], [[1k8g|1k8g]], [[1pa6|1pa6]], [[1ph1|1ph1]], [[1ph2|1ph2]], [[1ph3|1ph3]], [[1ph4|1ph4]], [[1ph5|1ph5]], [[1ph7|1ph7]], [[1ph8|1ph8]], [[1ph9|1ph9]], [[1phj|1phj]]
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ph6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ph6 OCA], [http://www.ebi.ac.uk/pdbsum/1ph6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ph6 RCSB]</span>
 }}
@@ Line 24: / Line 27: @@
 [[Category: Schultz, S C.]]
 [[Category: Theobald, D L.]]
-[[Category: NA]]
 [[Category: noncognate]]
 [[Category: ob fold]]
@@ Line 34: / Line 36: @@
 [[Category: telomere]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:24:16 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:59:38 2008''