1rfi: Difference between revisions

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-[[Image:1rfi.png|left|200px]]
-{{STRUCTURE_1rfi|  PDB=1rfi  |  SCENE=  }}
+==Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC==
+<StructureSection load='1rfi' size='340' side='right'caption='[[1rfi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-===Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC===
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rfi]] is a 6 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=1RFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RFI FirstGlance]. <br>
-{{ABSTRACT_PUBMED_14761185}}
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
-==About this Structure==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rfi OCA], [https://pdbe.org/1rfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rfi RCSB], [https://www.ebi.ac.uk/pdbsum/1rfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rfi ProSAT]</span></td></tr>
-[[1rfi]] is a 6 chain structure of [[Phosphodiesterase]] with 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=1RFI OCA].
+</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/rf/1rfi_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=1rfi ConSurf].
+<div style="clear:both"></div>
 ==See Also==
-*[[Phosphodiesterase|Phosphodiesterase]]
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:014761185</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Champoux, J J.]]
+[[Category: Large Structures]]
-[[Category: Davies, D R.]]
+[[Category: Champoux JJ]]
-[[Category: Hol, W G.]]
+[[Category: Davies DR]]
-[[Category: Interthal, H.]]
+[[Category: Hol WG]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Interthal H]]
-[[Category: Protein-dna complex]]
-[[Category: Transition state mimic.]]
-[[Category: Vanadate complex]]