2flp: Difference between revisions

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New page: left|200px<br /> <applet load="2flp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2flp, resolution 2.40Å" /> '''Binary complex of t...
 
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[[Image:2flp.gif|left|200px]]<br />
<applet load="2flp" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2flp, resolution 2.40&Aring;" />
'''Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)'''<br />


==Overview==
==Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)==
Substrate-induced conformational change of the protein is the linchpin of, enzymatic reactions. Replicative DNA polymerases, for example, convert, from an open to a closed conformation in response to dNTP binding. Human, DNA polymerase-iota (hPoliota), a member of the Y family of DNA, polymerases, differs strikingly from other polymerases in its much higher, proficiency and fidelity for nucleotide incorporation opposite template, purines than opposite template pyrimidines. We present here a, crystallographic analysis of hPoliota binary complexes, which together, with the ternary complexes show that, contrary to replicative DNA, polymerases, the DNA, and not the polymerase, undergoes the primary, substrate-induced conformational change. The incoming dNTP "pushes", templates A and G from the anti to the syn conformation dictated by a, rigid hPoliota active site. Together, the structures posit a mechanism for, template selection wherein dNTP binding induces a conformational switch in, template purines for productive Hoogsteen base pairing.
<StructureSection load='2flp' size='340' side='right'caption='[[2flp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2flp]] is a 3 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=2FLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FLP 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</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=2flp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2flp OCA], [https://pdbe.org/2flp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2flp RCSB], [https://www.ebi.ac.uk/pdbsum/2flp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2flp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</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/fl/2flp_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=2flp ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2FLP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. 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=2FLP OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
== References ==
==Reference==
<references/>
An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site., Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Structure. 2006 Apr;14(4):749-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16615915 16615915]
__TOC__
[[Category: DNA-directed DNA polymerase]]
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Aggarwal, A.K.]]
[[Category: Aggarwal AK]]
[[Category: Johnson, R.E.]]
[[Category: Johnson RE]]
[[Category: Nair, D.T.]]
[[Category: Nair DT]]
[[Category: Prakash, L.]]
[[Category: Prakash L]]
[[Category: Prakash, S.]]
[[Category: Prakash S]]
[[Category: binary complex]]
[[Category: dna polymerase]]
[[Category: lesion bypass]]
[[Category: template g]]
[[Category: y-family]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:07:10 2007''

Latest revision as of 12:24, 14 February 2024

Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)

Structural highlights

2flp is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POLI_HUMAN Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.[1] [2] [3] [4] [5] [6] [7]

Evolutionary Conservation

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

See Also

References

  1. ↑ Tissier A, Frank EG, McDonald JP, Iwai S, Hanaoka F, Woodgate R. Misinsertion and bypass of thymine-thymine dimers by human DNA polymerase iota. EMBO J. 2000 Oct 2;19(19):5259-66. PMID:11013228 doi:http://dx.doi.org/10.1093/emboj/19.19.5259
  2. ↑ Bebenek K, Tissier A, Frank EG, McDonald JP, Prasad R, Wilson SH, Woodgate R, Kunkel TA. 5'-Deoxyribose phosphate lyase activity of human DNA polymerase iota in vitro. Science. 2001 Mar 16;291(5511):2156-9. PMID:11251121 doi:http://dx.doi.org/10.1126/science.1058386
  3. ↑ Frank EG, Tissier A, McDonald JP, Rapic-Otrin V, Zeng X, Gearhart PJ, Woodgate R. Altered nucleotide misinsertion fidelity associated with poliota-dependent replication at the end of a DNA template. EMBO J. 2001 Jun 1;20(11):2914-22. PMID:11387224 doi:http://dx.doi.org/10.1093/emboj/20.11.2914
  4. ↑ Faili A, Aoufouchi S, Flatter E, Gueranger Q, Reynaud CA, Weill JC. Induction of somatic hypermutation in immunoglobulin genes is dependent on DNA polymerase iota. Nature. 2002 Oct 31;419(6910):944-7. PMID:12410315 doi:http://dx.doi.org/10.1038/nature01117
  5. ↑ Haracska L, Prakash L, Prakash S. A mechanism for the exclusion of low-fidelity human Y-family DNA polymerases from base excision repair. Genes Dev. 2003 Nov 15;17(22):2777-85. PMID:14630940 doi:10.1101/gad.1146103
  6. ↑ Washington MT, Minko IG, Johnson RE, Wolfle WT, Harris TM, Lloyd RS, Prakash S, Prakash L. Efficient and error-free replication past a minor-groove DNA adduct by the sequential action of human DNA polymerases iota and kappa. Mol Cell Biol. 2004 Jul;24(13):5687-93. PMID:15199127 doi:http://dx.doi.org/10.1128/MCB.24.13.5687-5693.2004
  7. ↑ Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature. 2004 Jul 15;430(6997):377-80. PMID:15254543 doi:10.1038/nature02692

2flp, resolution 2.40Å

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