3glf

From Proteopedia

(Difference between revisions)

Revision as of 08:26, 7 February 2016

Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA

Structural highlights

3glf is a 14 chain structure with sequence from Ecoli. The June 2012 RCSB PDB Molecule of the Month feature on Sliding Clamps by David Goodsell is 10.2210/rcsb_pdb/mom_2012_6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1sxj, 1jr3, 1xxh, 1xxi, 3glg, 3glh, 3gli
Gene:	holA, b0640, JW0635 (ECOLI), dnaX, dnaZ, dnaZX, b0470, JW0459 (ECOLI), holB, b1099, JW1085 (ECOLI)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[HOLA_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. The delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA. [HOLB_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. [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.

Publication Abstract from PubMed

Clamp loaders load sliding clamps onto primer-template DNA. The structure of the E. coli clamp loader bound to DNA reveals the formation of an ATP-dependent spiral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DNA primers. Unlike hexameric helicases, in which DNA translocation requires distinct conformations of the ATPase domains, the clamp loader spiral is symmetric and is set up to trigger release upon DNA recognition. Specificity for primed DNA arises from blockage of the end of the primer and accommodation of the emerging template along a surface groove. A related structure reveals how the psi protein, essential for coupling the clamp loader to single-stranded DNA-binding protein (SSB), binds to the clamp loader. By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex.

The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.,Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J Cell. 2009 May 15;137(4):659-71. PMID:19450514^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell. 2009 May 15;137(4):659-71. PMID:19450514 doi:10.1016/j.cell.2009.03.044

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3glf"

@@ Line 2: / Line 2: @@
 <StructureSection load='3glf' size='340' side='right' caption='[[3glf]], [[Resolution|resolution]] 3.39&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3glf]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. The June 2012 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Sliding Clamps''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2012_6 10.2210/rcsb_pdb/mom_2012_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GLF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3glf]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. The June 2012 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Sliding Clamps''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2012_6 10.2210/rcsb_pdb/mom_2012_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GLF FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1sxj|1sxj]], [[1jr3|1jr3]], [[1xxh|1xxh]], [[1xxi|1xxi]], [[3glg|3glg]], [[3glh|3glh]], [[3gli|3gli]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">holA, b0640, JW0635 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), dnaX, dnaZ, dnaZX, b0470, JW0459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), holB, b1099, JW1085 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">holA, b0640, JW0635 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), dnaX, dnaZ, dnaZX, b0470, JW0459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), holB, b1099, JW1085 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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='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=3glf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3glf RCSB], [http://www.ebi.ac.uk/pdbsum/3glf PDBsum]</span></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=3glf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glf OCA], [http://pdbe.org/3glf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3glf RCSB], [http://www.ebi.ac.uk/pdbsum/3glf PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 19: @@
     <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=3glf ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3glf" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 37: / Line 38: @@
 </StructureSection>
 [[Category: DNA-directed DNA polymerase]]
-[[Category: Escherichia coli k-12]]
+[[Category: Ecoli]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Sliding Clamps]]

3glf

From Proteopedia

Revision as of 08:26, 7 February 2016

Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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