1d4u: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1d4u.png|left|200px]]
-<!--
+==INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES==
-The line below this paragraph, containing "STRUCTURE_1d4u", creates the "Structure Box" on the page.
+<StructureSection load='1d4u' size='340' side='right'caption='[[1d4u]]' 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'>[[1d4u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D4U 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">Solution NMR</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1d4u|  PDB=1d4u  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d4u OCA], [https://pdbe.org/1d4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d4u RCSB], [https://www.ebi.ac.uk/pdbsum/1d4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d4u ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/XPA_HUMAN XPA_HUMAN] Defects in XPA are a cause of xeroderma pigmentosum complementation group A (XP-A) [MIM:[https://omim.org/entry/278700 278700]; also known as xeroderma pigmentosum type 1 (XP1). XP-A is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities. Group A patients show the most severe skin symptoms and progressive neurological disorders.<ref>PMID:1339397</ref> <ref>PMID:1372103</ref> <ref>PMID:9671271</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/XPA_HUMAN XPA_HUMAN] Involved in DNA excision repair. Initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. Required for UV-induced CHEK1 phosphorylation and the recruitment of CEP164 to cyclobutane pyrimidine dimmers (CPD), sites of DNA damage after UV irradiation.<ref>PMID:19197159</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/d4/1d4u_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=1d4u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human XPA is an essential component in the multienzyme nucleotide excision repair (NER) pathway. The solution structure of the minimal DNA binding domain of XPA (XPA-MBD: M98-F219) was recently determined [Buchko et al. (1998) Nucleic Acids Res. 26, 2779-2788, Ikegami et al. (1998) Nat. Struct. Biol. 5, 701-706] and shown to consist of a compact zinc-binding core and a loop-rich C-terminal subdomain connected by a linker sequence. Here, the solution structure of XPA-MBD was further refined using an entirely new class of restraints based on pseudocontact shifts measured in cobalt-substituted XPA-MBD. Using this structure, the surface of XPA-MBD which interacts with DNA and a fragment of the largest subunit of replication protein A (RPA70 Delta C327: M1-Y326) was determined using chemical shift mapping. DNA binding in XPA-MBD was highly localized in the loop-rich subdomain for DNA with or without a lesion [dihydrothymidine (dhT) or 6-4-thymidine-cytidine (64TC)], or with DNA in single- or double-stranded form, indicating that the character of the lesion itself is not the driving force for XPA binding DNA. RPA70 Delta C327 was found to contact regions in both the zinc-binding and loop-rich subdomains. Some overlap of the DNA and RPA70 Delta C327 binding regions was observed in the loop-rich subdomain, indicating a possible cooperative DNA-binding mode between XPA and RPA70 Delta C327. To complement the chemical shift mapping data, the backbone dynamics of free XPA-MBD and XPA-MBD bound to DNA oligomers containing dhT or 64TC lesions were investigated using 15N NMR relaxation data. The dynamic analyses for the XPA-MBD complexes with DNA revealed localized increases and decreases in S2 and an increase in the global correlation time. Regions of XPA-MBD with the largest increases in S2 overlapped regions having the largest chemical shifts changes upon binding DNA, indicating that the loop-rich subdomain becomes more rigid upon binding DNA. Interestingly, S2 decreased for some residues in the zinc-binding core upon DNA association, indicating a possible concerted structural rearrangement on binding DNA.
-===INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES===
+Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies.,Buchko GW, Daughdrill GW, de Lorimier R, Rao B K, Isern NG, Lingbeck JM, Taylor JS, Wold MS, Gochin M, Spicer LD, Lowry DF, Kennedy MA Biochemistry. 1999 Nov 16;38(46):15116-28. PMID:10563794<ref>PMID:10563794</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10563794}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1d4u" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10563794 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10563794}}
+__TOC__
+</StructureSection>
-==About this Structure==
-D4U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4U OCA].
-==Reference==
-Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies., Buchko GW, Daughdrill GW, de Lorimier R, Rao B K, Isern NG, Lingbeck JM, Taylor JS, Wold MS, Gochin M, Spicer LD, Lowry DF, Kennedy MA, Biochemistry. 1999 Nov 16;38(46):15116-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10563794 10563794]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Buchko, G W.]]
+[[Category: Buchko GW]]
-[[Category: Daughdrill, G W.]]
+[[Category: Daughdrill GW]]
-[[Category: Gochin, M.]]
+[[Category: Gochin M]]
-[[Category: Isern, N G.]]
+[[Category: Isern NG]]
-[[Category: Kennedy, M A.]]
+[[Category: Kennedy MA]]
-[[Category: Lingbeck, J.]]
+[[Category: Lingbeck J]]
-[[Category: Lorimier, R de.]]
+[[Category: Lowry DF]]
-[[Category: Lowry, D F.]]
+[[Category: Rao S]]
-[[Category: Rao, S.]]
+[[Category: Spicer LD]]
-[[Category: Spicer, L D.]]
+[[Category: Taylor J]]
-[[Category: Taylor, J.]]
+[[Category: Wold MS]]
-[[Category: Wold, M S.]]
+[[Category: De Lorimier R]]
-[[Category: Dna repair]]
-[[Category: Loop-rich domain]]
-[[Category: Nmr relaxation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:25:15 2008''