1kfd: Difference between revisions

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 ==CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE==
-<StructureSection load='1kfd' size='340' side='right' caption='[[1kfd]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+<StructureSection load='1kfd' size='340' side='right'caption='[[1kfd]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1kfd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KFD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1kfd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KFD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.9&#8491;</td></tr>
-<tr id='activity'><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 id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kfd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kfd RCSB], [http://www.ebi.ac.uk/pdbsum/1kfd PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kfd OCA], [https://pdbe.org/1kfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kfd RCSB], [https://www.ebi.ac.uk/pdbsum/1kfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kfd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPO1_ECOLI DPO1_ECOLI]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template.
+[https://www.uniprot.org/uniprot/DPO1_ECOLI DPO1_ECOLI] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template.
 == 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/kf/1kfd_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/1kfd_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].
+</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=1kfd ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Crystal structures of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli complexed with deoxynucleoside triphosphate (dNTP) or with pyrophosphate (PPi) determined to 3.9-A resolution by X-ray crystallography show these molecules binding within the cleft of the polymerase domain and surrounded by residues previously implicated in dNTP binding. The dNTP binds adjacent to the O-helix [Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., &amp; Steitz, T. A. (1985a) Nature 313, 762-766] with its triphosphate moiety anchored by three positively charged residues, Arg 754, Arg 682, and Lys 758, plus His 734 and Gln 708. The dNTP binding site observed in the crystal is consistent with the results of chemical modification including cross-linking and is also near many of the amino acid residues whose mutation affects catalysis [Polesky, A. H., Steitz, T. A., Grindley, N. D. F., &amp; Joyce, C. M. (1990) J. Biol. Chem. 265, 14579-14591; Polesky, A. H., Dahlberg, M. E., Benkovic, S. J., Grindley, N. D. F., &amp; Joyce, C. M. (1992) J. Biol. Chem. 267, 8417-8428]. However, we conclude that the position of at least the dNMP moiety of dNTP in the binary complex is not likely to be the same as in its catalytically relevant complex with primer-template DNA.
-Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate.,Beese LS, Friedman JM, Steitz TA Biochemistry. 1993 Dec 28;32(51):14095-101. PMID:8260491<ref>PMID:8260491</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Escherichia coli]]
-[[Category: Beese, L S]]
+[[Category: Large Structures]]
-[[Category: Friedman, J M]]
+[[Category: Beese LS]]
-[[Category: Steitz, T A]]
+[[Category: Friedman JM]]
-[[Category: Nucleotidyltransferase]]
+[[Category: Steitz TA]]