3u60

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(Difference between revisions)

Revision as of 05:59, 13 July 2022

Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog

Structural highlights

3u60 is a 10 chain structure with sequence from Bpt4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	1czd, 1sxj, 3glf, 1jr3, 1xxh, 3u5z, 3u61
Gene:	44, gp44 (BPT4), 62, gp62 (BPT4), 45, gp45 (BPT4)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPA62_BPT4] Function as a sliding-clamp-loading ATPase enzyme during DNA replication. Required for elongation of primed templates by controlling the polymerase processivity. Progressive binding of ATPs triggers a conformational change in the complex that inhibits ATPase activity. [DPA44_BPT4] Function as a sliding-clamp-loading ATPase enzyme during DNA replication. Required for elongation of primed templates by controlling the polymerase processivity. Possesses DNA-dependent ATPase activity on its own and within the heterodimer gp44/gp62. Progressive binding of ATPs triggers a conformational change in the complex that inhibits ATPase activity.^[1] ^[2] [DPA5_BPT4] Replisome sliding clamp subunit. Responsible for tethering the catalytic subunit of DNA polymerase to DNA during high-speed replication.

Publication Abstract from PubMed

Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.

How a DNA polymerase clamp loader opens a sliding clamp.,Kelch BA, Makino DL, O'Donnell M, Kuriyan J Science. 2011 Dec 23;334(6063):1675-80. PMID:22194570^[3]

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

References

↑ Zhuang Z, Berdis AJ, Benkovic SJ. An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex. Biochemistry. 2006 Jul 4;45(26):7976-89. PMID:16800623 doi:http://dx.doi.org/10.1021/bi0601205
↑ Pietroni P, von Hippel PH. Multiple ATP binding is required to stabilize the "activated" (clamp open) clamp loader of the T4 DNA replication complex. J Biol Chem. 2008 Oct 17;283(42):28338-53. doi: 10.1074/jbc.M804371200. Epub 2008, Aug 1. PMID:18676368 doi:http://dx.doi.org/10.1074/jbc.M804371200
↑ Kelch BA, Makino DL, O'Donnell M, Kuriyan J. How a DNA polymerase clamp loader opens a sliding clamp. Science. 2011 Dec 23;334(6063):1675-80. PMID:22194570 doi:10.1126/science.1211884

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3u60"

@@ Line 1: / Line 1: @@
 ==Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog==
-<StructureSection load='3u60' size='340' side='right' caption='[[3u60]], [[Resolution|resolution]] 3.34&Aring;' scene=''>
+<StructureSection load='3u60' size='340' side='right'caption='[[3u60]], [[Resolution|resolution]] 3.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3u60]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U60 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U60 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3u60]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U60 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U60 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=08T:[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-TRIS(FLUORANYL)BERYLLIUM'>08T</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=08T:[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-TRIS(FLUORANYL)BERYLLIUM'>08T</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1czd|1czd]], [[1sxj|1sxj]], [[3glf|3glf]], [[1jr3|1jr3]], [[1xxh|1xxh]], [[3u5z|3u5z]], [[3u61|3u61]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1czd|1czd]], [[1sxj|1sxj]], [[3glf|3glf]], [[1jr3|1jr3]], [[1xxh|1xxh]], [[3u5z|3u5z]], [[3u61|3u61]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">44, gp44 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4]), 62, gp62 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4]), 45, gp45 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">44, gp44 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4]), 62, gp62 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4]), 45, gp45 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=3u60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u60 OCA], [http://pdbe.org/3u60 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u60 RCSB], [http://www.ebi.ac.uk/pdbsum/3u60 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u60 ProSAT]</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=3u60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u60 OCA], [https://pdbe.org/3u60 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u60 RCSB], [https://www.ebi.ac.uk/pdbsum/3u60 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u60 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPA62_BPT4 DPA62_BPT4]] Function as a sliding-clamp-loading ATPase enzyme during DNA replication. Required for elongation of primed templates by controlling the polymerase processivity. Progressive binding of ATPs triggers a conformational change in the complex that inhibits ATPase activity. [[http://www.uniprot.org/uniprot/DPA44_BPT4 DPA44_BPT4]] Function as a sliding-clamp-loading ATPase enzyme during DNA replication. Required for elongation of primed templates by controlling the polymerase processivity. Possesses DNA-dependent ATPase activity on its own and within the heterodimer gp44/gp62. Progressive binding of ATPs triggers a conformational change in the complex that inhibits ATPase activity.<ref>PMID:16800623</ref> <ref>PMID:18676368</ref>  [[http://www.uniprot.org/uniprot/DPA5_BPT4 DPA5_BPT4]] Replisome sliding clamp subunit. Responsible for tethering the catalytic subunit of DNA polymerase to DNA during high-speed replication.
+[[https://www.uniprot.org/uniprot/DPA62_BPT4 DPA62_BPT4]] Function as a sliding-clamp-loading ATPase enzyme during DNA replication. Required for elongation of primed templates by controlling the polymerase processivity. Progressive binding of ATPs triggers a conformational change in the complex that inhibits ATPase activity. [[https://www.uniprot.org/uniprot/DPA44_BPT4 DPA44_BPT4]] Function as a sliding-clamp-loading ATPase enzyme during DNA replication. Required for elongation of primed templates by controlling the polymerase processivity. Possesses DNA-dependent ATPase activity on its own and within the heterodimer gp44/gp62. Progressive binding of ATPs triggers a conformational change in the complex that inhibits ATPase activity.<ref>PMID:16800623</ref> <ref>PMID:18676368</ref>  [[https://www.uniprot.org/uniprot/DPA5_BPT4 DPA5_BPT4]] Replisome sliding clamp subunit. Responsible for tethering the catalytic subunit of DNA polymerase to DNA during high-speed replication.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 </StructureSection>
 [[Category: Bpt4]]
+[[Category: Large Structures]]
 [[Category: Donnell, M O]]
 [[Category: Kelch, B A]]

3u60

From Proteopedia

Revision as of 05:59, 13 July 2022

Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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