1njf: Difference between revisions

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New page: left|200px<br /><applet load="1njf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1njf, resolution 2.30Å" /> '''Nucleotide bound for...
 
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[[Image:1njf.gif|left|200px]]<br /><applet load="1njf" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1njf, resolution 2.30&Aring;" />
'''Nucleotide bound form of an isolated E. coli clamp loader gamma subunit'''<br />


==Overview==
==Nucleotide bound form of an isolated E. coli clamp loader gamma subunit==
Sliding clamps are loaded onto DNA by ATP-driven clamp loader complexes., The structure of the E. coli clamp loader in a nucleotide-free state has, been determined previously. We now report crystal structures of a, truncated form of the isolated gamma-ATPase subunit, gamma(1-243), of the, E. coli clamp loader, in nucleotide-free and bound forms. The gamma, subunit adopts a defined conformation when empty, in which the nucleotide, binding site is blocked. The binding of either ATPgammaS or ADP, which are, shown to bind with equal affinity to gamma(1-243), induces a change in the, relative orientation of the two domains such that nucleotides can be, accommodated. This change would break one of the gamma:gamma interfaces, seen in the empty clamp loader complex, and may represent one step in the, activation process.
<StructureSection load='1njf' size='340' side='right'caption='[[1njf]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1njf]] is a 4 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=1NJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJF 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]] 2.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1njf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njf OCA], [https://pdbe.org/1njf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njf RCSB], [https://www.ebi.ac.uk/pdbsum/1njf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPO3X_ECOLI DPO3X_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity.  Isoform tau: serves as a scaffold to help in the dimerization of the core complex.  Isoform gamma: seems to interact with the delta subunit. to transfer the beta subunit on the DNA.
== 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/nj/1njf_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=1njf ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1NJF 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 ZN, ATG and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1NJF OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit., Podobnik M, Weitze TF, O'Donnell M, Kuriyan J, Structure. 2003 Mar;11(3):253-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12623013 12623013]
[[Category: DNA-directed DNA polymerase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Donnell, M.O.]]
[[Category: Kuriyan J]]
[[Category: Kuriyan, J.]]
[[Category: O'Donnell M]]
[[Category: Podobnik, M.]]
[[Category: Podobnik M]]
[[Category: Weitze, T.F.]]
[[Category: Weitze TF]]
[[Category: ADP]]
[[Category: ATG]]
[[Category: ZN]]
[[Category: aaa+ atpase domains]]
[[Category: protein-nucleotide complex]]
[[Category: rossman-like fold]]
[[Category: sensor 1]]
[[Category: sensor 2]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:18:58 2007''

Latest revision as of 10:57, 14 February 2024

Nucleotide bound form of an isolated E. coli clamp loader gamma subunitNucleotide bound form of an isolated E. coli clamp loader gamma subunit

Structural highlights

1njf is a 4 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 2.3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3X_ECOLI DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. Isoform tau: serves as a scaffold to help in the dimerization of the core complex. Isoform gamma: seems to interact with the delta subunit. to transfer the beta subunit on the DNA.

Evolutionary Conservation

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

See Also

1njf, resolution 2.30Å

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