1kfd: Difference between revisions

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New page: left|200px<br /><applet load="1kfd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kfd, resolution 3.9Å" /> '''CRYSTAL STRUCTURES OF...
 
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[[Image:1kfd.jpg|left|200px]]<br /><applet load="1kfd" size="450" color="white" frame="true" align="right" spinBox="true"
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'''CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE'''<br />


==Overview==
==CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE==
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.
<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 [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='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='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'>[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 ==
[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>
    <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=1kfd ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KFD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CTP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KFD OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8260491 8260491]
[[Category: DNA-directed DNA polymerase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Beese, L.S.]]
[[Category: Beese LS]]
[[Category: Friedman, J.M.]]
[[Category: Friedman JM]]
[[Category: Steitz, T.A.]]
[[Category: Steitz TA]]
[[Category: CTP]]
[[Category: nucleotidyltransferase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:09:35 2007''

Latest revision as of 10:46, 7 February 2024

CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATECRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE

Structural highlights

1kfd is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1kfd, resolution 3.90Å

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