1okb

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{{Seed}}
 
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[[Image:1okb.png|left|200px]]
 
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==crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)==
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The line below this paragraph, containing "STRUCTURE_1okb", creates the "Structure Box" on the page.
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<StructureSection load='1okb' size='340' side='right'caption='[[1okb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1okb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gadus_morhua Gadus morhua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OKB FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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{{STRUCTURE_1okb| PDB=1okb | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1okb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okb OCA], [https://pdbe.org/1okb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1okb RCSB], [https://www.ebi.ac.uk/pdbsum/1okb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1okb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9I983_GADMO Q9I983_GADMO] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).[RuleBase:RU003780][HAMAP-Rule:MF_03166]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/1okb_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1okb ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Uracil-DNA glycosylase (UDG; EC 3.2.2.3) is a DNA-repair protein that catalyses the hydrolysis of promutagenic uracil residues from single- or double-stranded DNA, generating free uracil and abasic DNA. The crystal structure of the catalytic domain of cod uracil-DNA glycosylase (cUDG) has been determined to 1.9 A resolution, with final R factors of 18.61 and 20.57% for the working and test sets of reflections, respectively. This is the first crystal structure of a uracil-DNA glycosylase from a cold-adapted species and a detailed comparison with the human enzyme is performed in order to rationalize the cold-adapted behaviour of the cod enzyme at the structural level. The catalytic domain of cUDG comprises 223 residues, with a sequence identity to the human UDG of 75%. The tertiary structures of the two enzymes are also similar, with an overall displacement in main-chain atomic positions of 0.63 A. The amino-acid substitutions and the differences in intramolecular hydrogen bonds, hydrophobic interactions, ion-pair interactions and electrostatic potentials are compared and discussed in order to gain insight into the factors that cause the increased activity and reduced thermostability of the cod enzyme. In particular, the reduced number of strong ion-pair interactions in the C-terminal half of cUDG is believed to greatly affect the flexibility and/or stability. Increased positive electrostatic surface potential on the DNA-facing side of cUDG seems to be responsible for increasing the affinity for the negatively charged DNA compared with that of hUDG.
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===CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM ATLANTIC COD (GADUS MORHUA)===
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The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.,Leiros I, Moe E, Lanes O, Smalas AO, Willassen NP Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1357-65. Epub 2003, Jul 23. PMID:12876336<ref>PMID:12876336</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1okb" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12876336}}, adds the Publication Abstract to the page
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12876336 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12876336}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1OKB is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Gadus_morhua Gadus morhua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKB OCA].
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==Reference==
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<ref group="xtra">PMID:12876336</ref><references group="xtra"/>
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[[Category: Gadus morhua]]
[[Category: Gadus morhua]]
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[[Category: Uridine nucleosidase]]
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[[Category: Large Structures]]
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[[Category: Lanes, O.]]
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[[Category: Lanes O]]
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[[Category: Leiros, I.]]
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[[Category: Leiros I]]
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[[Category: Moe, E.]]
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[[Category: Moe E]]
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[[Category: Smalas, A O.]]
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[[Category: Smalas AO]]
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[[Category: Willassen, N P.]]
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[[Category: Willassen NP]]
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[[Category: Base excision repair]]
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[[Category: Cold-adaptation]]
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[[Category: Crystal structure]]
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[[Category: Hydrolase]]
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[[Category: Structure-function relationship]]
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[[Category: Uracil-dna glycosylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:20:39 2009''
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Current revision

crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)

PDB ID 1okb

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