3gdx

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{{Seed}}
 
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[[Image:3gdx.jpg|left|200px]]
 
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==Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP==
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The line below this paragraph, containing "STRUCTURE_3gdx", creates the "Structure Box" on the page.
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<StructureSection load='3gdx' size='340' side='right'caption='[[3gdx]], [[Resolution|resolution]] 2.20&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'>[[3gdx]] is a 4 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=3GDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDX 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]] 2.2&#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=4BD:5-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>4BD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3gdx| PDB=3gdx | 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=3gdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdx OCA], [https://pdbe.org/3gdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gdx RCSB], [https://www.ebi.ac.uk/pdbsum/3gdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] 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.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
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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/gd/3gdx_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=3gdx 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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Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.
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===Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP===
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Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function.,Upton TG, Kashemirov BA, McKenna CE, Goodman MF, Prakash GK, Kultyshev R, Batra VK, Shock DD, Pedersen LC, Beard WA, Wilson SH Org Lett. 2009 May 7;11(9):1883-6. PMID:19351147<ref>PMID:19351147</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 3gdx" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19351147}}, adds the Publication Abstract to the page
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19351147 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19351147}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3GDX is a 4 chains structure of sequences 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=3GDX OCA].
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==Reference==
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<ref group="xtra">PMID:19351147</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Batra, V K.]]
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[[Category: Large Structures]]
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[[Category: Pedersen, L C.]]
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[[Category: Batra VK]]
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[[Category: Wilson, S H.]]
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[[Category: Pedersen LC]]
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[[Category: Dna damage]]
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[[Category: Wilson SH]]
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[[Category: Dna polymerase]]
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[[Category: Dna repair]]
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[[Category: Dna replication]]
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[[Category: Dna synthesis]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed dna polymerase]]
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[[Category: Lyase]]
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[[Category: Magnesium]]
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[[Category: Metal-binding]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Nucleus]]
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[[Category: Nucloetidyl transferase]]
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[[Category: Polymorphism]]
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[[Category: Sodium]]
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[[Category: Transferase]]
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[[Category: Transferase/dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 09:57:18 2009''
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Current revision

Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP

PDB ID 3gdx

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