1nom: Difference between revisions

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-{{STRUCTURE_1nom|  PDB=1nom  |  SCENE=  }}
+==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR)==
-===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR)===
+<StructureSection load='1nom' size='340' side='right' caption='[[1nom]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-{{ABSTRACT_PUBMED_8841120}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NOM FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[7ice|7ice]], [[7icf|7icf]], [[7icg|7icg]], [[7ich|7ich]], [[7ici|7ici]], [[7icj|7icj]], [[7ick|7ick]], [[7icl|7icl]], [[7icm|7icm]], [[7icn|7icn]], [[7ico|7ico]], [[7icp|7icp]], [[7icq|7icq]], [[7icr|7icr]], [[7ics|7ics]], [[7ict|7ict]], [[7icu|7icu]], [[7icv|7icv]], [[8ica|8ica]], [[8icb|8icb]], [[8icc|8icc]], [[8ice|8ice]], [[8icf|8icf]], [[8icg|8icg]], [[8ich|8ich]], [[8ici|8ici]], [[8icj|8icj]], [[8ick|8ick]], [[8icl|8icl]], [[8icm|8icm]], [[8icn|8icn]], [[8ico|8ico]], [[8icp|8icp]], [[8icq|8icq]], [[8icr|8icr]], [[8ics|8ics]], [[8ict|8ict]], [[8icu|8icu]], [[8icv|8icv]], [[8icw|8icw]], [[8icx|8icx]], [[8icy|8icy]], [[8icz|8icz]], [[9ica|9ica]], [[9icb|9icb]], [[9icc|9icc]], [[9ice|9ice]], [[9icf|9icf]], [[9icg|9icg]], [[9ich|9ich]], [[9ici|9ici]], [[9icj|9icj]], [[9ick|9ick]], [[9icl|9icl]], [[9icm|9icm]], [[9icn|9icn]], [[9ico|9ico]], [[9icp|9icp]], [[9icq|9icq]], [[9icr|9icr]], [[9ics|9ics]], [[9ict|9ict]], [[9icu|9icu]], [[9icv|9icv]], [[9icw|9icw]], [[9icx|9icx]], [[9icy|9icy]], [[1zqa|1zqa]], [[1zqb|1zqb]], [[1zqc|1zqc]], [[1zqd|1zqd]], [[1zqe|1zqe]], [[1zqf|1zqf]], [[1zqg|1zqg]], [[1zqh|1zqh]], [[1zqi|1zqi]], [[1zqj|1zqj]], [[1zqk|1zqk]], [[1zql|1zql]], [[1zqm|1zqm]], [[1zqn|1zqn]], [[1zqo|1zqo]], [[1zqp|1zqp]], [[1zqq|1zqq]], [[1zqr|1zqr]], [[1zqs|1zqs]], [[1zqt|1zqt]], [[1bcb|1bcb]], [[2bcc|2bcc]], [[1bcd|1bcd]], [[1bce|1bce]], [[2bpf|2bpf]], [[2bpg|2bpg]], [[1zqu|1zqu]], [[1zqv|1zqv]], [[1zqw|1zqw]], [[1zqx|1zqx]], [[1zqy|1zqy]], [[1zqz|1zqz]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nom RCSB], [http://www.ebi.ac.uk/pdbsum/1nom PDBsum]</span></td></tr>
+<table>
+== 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/1nom_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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+X-ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix-hairpin-helix (HhH) motifs, one in the fingers subdomain and the other in the 8-kDa domain [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., &amp; Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA binding by each HhH motif is facilitated by a metal ion, we set out to determine the identity of the metal ion that most likely binds to the HhH motif in vivo. Crystal soaking experiments were performed on human pol beta-DNA cocrystals with Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in each case a data set was collected and the resulting structure was refined. Under the conditions tested, the HhH motifs of pol beta have an affinity for these biologically prevalent metal ions in the order Mg2+ &lt; Ca2+ &lt; Na+ &lt; K+, with K+ displaying the strongest binding. Crystals soaked in the presence of Tl+, a commonly used spectroscopic probe for K+, were too X-ray-sensitive to establish the binding behavior of Tl+, but soaking experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave evidence of metal ion binding in both HhH motifs, confirming that larger monovalent and divalent metal ions are capable of binding to the HhH metal sites. Although Mn2+, which has been categorized as a potent polymerase mutagen, binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to the HhH motifs in the presence of equimolar concentrations of Na+. These results suggest that in vivo, where Mn2+ is present only in trace amounts, Mn2+ probably does not have a large effect on DNA binding and may instead manifest a mutagenic effect on pol beta primarily by distorting nucleotide binding or by directly affecting the catalytic step [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., &amp; Kraut, J. (1996b) Biochemistry 35, 12762-12777]. Crystal soaking experiments with 31-kDa apoenzyme crystals show that, in the absence of DNA, the HhH motif in the fingers subdomain binds metal ions with either much lower occupancy or not at all, indicating that metal ion binding is dependent on the presence of the DNA substrate.
-==Function==
+Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.,Pelletier H, Sawaya MR Biochemistry. 1996 Oct 1;35(39):12778-87. PMID:8841120<ref>PMID:8841120</ref>
-[[http://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[1nom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NOM OCA].
+</div>
 ==See Also==
 *[[DNA polymerase|DNA polymerase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:008841120</ref><references group="xtra"/><references/>
+__TOC__
+</StructureSection>
 [[Category: DNA-directed DNA polymerase]]
 [[Category: Rattus norvegicus]]