1uvh: Difference between revisions

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-{{Seed}}
-[[Image:1uvh.png|left|200px]]
-<!--
+==X-ray structure of Dps from Mycobacterium smegmatis==
-The line below this paragraph, containing "STRUCTURE_1uvh", creates the "Structure Box" on the page.
+<StructureSection load='1uvh' size='340' side='right'caption='[[1uvh]], [[Resolution|resolution]] 2.80&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'>[[1uvh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UVH 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-{{STRUCTURE_1uvh|  PDB=1uvh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uvh OCA], [https://pdbe.org/1uvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uvh RCSB], [https://www.ebi.ac.uk/pdbsum/1uvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uvh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPS_MYCSM DPS_MYCSM] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). It protects DNA from hydroxyl radical-mediated cleavage. Binds DNA with no apparent sequence specificity without self-aggregation nor promotion of DNA condensation. Is unable to protect DNA from DNase-mediated cleavage.<ref>PMID:12466274</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/uv/1uvh_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=1uvh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure and function of Mycobacterium smegmatis Dps (DNA-binding proteins from starved cells) and of the protein studied by Gupta and Chatterji, in which the C terminus that is used for binding DNA contains a histidine tag, have been characterized in parallel. The native dodecamer dissociated reversibly into dimers above pH 7.5 and below pH 6.0, with apparent pK(a) values of approximately 7.65 and 4.75; at pH approximately 4.0, dimers formed monomers. Based on structural analysis, the two dissociation steps have been attributed to breakage of the salt bridges between Glu(157) and Arg(99) located at the 3-fold symmetry axes and to protonation of Asp(66) hydrogen-bonded to Lys(36) across the dimer interface, respectively. The C-terminal tag did not affect subunit dissociation, but altered DNA binding dramatically. At neutral pH, protonation of the histidine tag promoted DNA condensation, whereas in the native C terminus, compensation of negative and positive charges led to DNA binding without condensation. This different mode of interaction with DNA has important functional consequences as indicated by the failure of the native protein to protect DNA from DNase-mediated cleavage and by the efficiency of the tagged protein in doing so as a result of DNA sequestration in the condensates. Chemical protection of DNA from oxidative damage is realized by Dps proteins in a multistep iron oxidation/uptake/mineralization process. Dimers have a decreased protection efficiency due to disruption of the dodecamer internal cavity, where iron is deposited and mineralized after oxidation at the ferroxidase center.
-===X-RAY STRUCTURE OF DPS FROM MYCOBACTERIUM SMEGMATIS===
+Reassessment of protein stability, DNA binding, and protection of Mycobacterium smegmatis Dps.,Ceci P, Ilari A, Falvo E, Giangiacomo L, Chiancone E J Biol Chem. 2005 Oct 14;280(41):34776-85. Epub 2005 Jul 19. PMID:16030020<ref>PMID:16030020</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1uvh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16030020}}, adds the Publication Abstract to the page
+*[[Ferritin 3D structures|Ferritin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16030020 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16030020}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-UVH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UVH OCA].
+[[Category: Mycolicibacterium smegmatis]]
+[[Category: Ceci P]]
-==Reference==
+[[Category: Chiancone E]]
-Reassessment of protein stability, DNA binding, and protection of Mycobacterium smegmatis Dps., Ceci P, Ilari A, Falvo E, Giangiacomo L, Chiancone E, J Biol Chem. 2005 Oct 14;280(41):34776-85. Epub 2005 Jul 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16030020 16030020]
+[[Category: Falvo E]]
-[[Category: Mycobacterium smegmatis]]
+[[Category: Ilari A]]
-[[Category: Single protein]]
-[[Category: Ceci, P.]]
-[[Category: Chiancone, E.]]
-[[Category: Falvo, E.]]
-[[Category: Ilari, A.]]
-[[Category: Dna binding protein]]
-[[Category: Dna protection from oxidative damage]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:24:10 2008''