1nop

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:58, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1nop.png|left|200px]]
 
-
<!--
+
==Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide==
-
The line below this paragraph, containing "STRUCTURE_1nop", creates the "Structure Box" on the page.
+
<StructureSection load='1nop' size='340' side='right'caption='[[1nop]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1nop]] is a 5 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=1NOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NOP FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
-
{{STRUCTURE_1nop| PDB=1nop | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nop OCA], [https://pdbe.org/1nop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nop RCSB], [https://www.ebi.ac.uk/pdbsum/1nop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nop ProSAT]</span></td></tr>
 +
</table>
 +
== Disease ==
 +
[https://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN] Defects in TDP1 are the cause of spinocerebellar ataxia autosomal recessive with axonal neuropathy (SCAN1) [MIM:[https://omim.org/entry/607250 607250]. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence.<ref>PMID:16141202</ref> <ref>PMID:15647511</ref> <ref>PMID:12244316</ref> <ref>PMID:17948061</ref> <ref>PMID:15920477</ref>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.<ref>PMID:12023295</ref> <ref>PMID:15111055</ref> <ref>PMID:15811850</ref> <ref>PMID:16141202</ref> <ref>PMID:22822062</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/1nop_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1nop ConSurf].
 +
<div style="clear:both"></div>
-
===Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide===
+
==See Also==
-
 
+
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
-
 
+
== References ==
-
<!--
+
<references/>
-
The line below this paragraph, {{ABSTRACT_PUBMED_12618186}}, adds the Publication Abstract to the page
+
__TOC__
-
(as it appears on PubMed at http://www.pubmed.gov), where 12618186 is the PubMed ID number.
+
</StructureSection>
-
-->
+
-
{{ABSTRACT_PUBMED_12618186}}
+
-
 
+
-
==About this Structure==
+
-
1NOP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOP OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide., Davies DR, Interthal H, Champoux JJ, Hol WG, Chem Biol. 2003 Feb;10(2):139-47. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12618186 12618186]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Champoux, J J.]]
+
[[Category: Champoux JJ]]
-
[[Category: Davies, D R.]]
+
[[Category: Davies DR]]
-
[[Category: Hol, W G.J.]]
+
[[Category: Hol WGJ]]
-
[[Category: Interthal, H.]]
+
[[Category: Interthal H]]
-
[[Category: Protein-dna complex]]
+
-
[[Category: Transition state mimic]]
+
-
[[Category: Vanadate complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 10:16:14 2008''
+

Current revision

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

PDB ID 1nop

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nop"
Personal tools