6drt

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

Structural highlights

6drt is a 6 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.117Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLAMP_BPT4 Sliding clamp that encircles the genomic DNA and links the DNA polymerase to the template to control the processivity of DNA synthesis. Responsible for tethering the catalytic subunit of DNA polymerase to DNA during high-speed replication (PubMed:10535942). Interaction with the sliding-clamp-loader opens the sliding clamp so that it can be loaded around the DNA template (PubMed:22194570). During transcription, encircles the DNA and tethers host RNA polymerase (RNAP) to it (PubMed:33602900).[HAMAP-Rule:MF_04161]^[1] ^[2] ^[3]

Publication Abstract from PubMed

DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact alpha-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel alpha-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.

T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.,Shi K, Bohl TE, Park J, Zasada A, Malik S, Banerjee S, Tran V, Li N, Yin Z, Kurniawan F, Orellana K, Aihara H Nucleic Acids Res. 2018 Aug 29. pii: 5085977. doi: 10.1093/nar/gky776. PMID:30169742^[4]

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

References

↑ Latham GJ, Dong F, Pietroni P, Dozono JM, Bacheller DJ, von Hippel PH. Opening of a monomer-monomer interface of the trimeric bacteriophage T4-coded GP45 sliding clamp is required for clamp loading onto DNA. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12448-53. PMID:10535942 doi:10.1073/pnas.96.22.12448
↑ 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
↑ Shi J, Wen A, Jin S, Gao B, Huang Y, Feng Y. Transcription activation by a sliding clamp. Nat Commun. 2021 Feb 18;12(1):1131. PMID:33602900 doi:10.1038/s41467-021-21392-0
↑ Shi K, Bohl TE, Park J, Zasada A, Malik S, Banerjee S, Tran V, Li N, Yin Z, Kurniawan F, Orellana K, Aihara H. T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Nucleic Acids Res. 2018 Aug 29. pii: 5085977. doi: 10.1093/nar/gky776. PMID:30169742 doi:http://dx.doi.org/10.1093/nar/gky776

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6drt"

Categories: Escherichia virus T4 | Large Structures | Aihara H | Shi K

@@ Line 1: / Line 1: @@
 ==Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4==
-<StructureSection load='6drt' size='340' side='right' caption='[[6drt]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
+<StructureSection load='6drt' size='340' side='right'caption='[[6drt]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6drt]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DRT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6drt]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DRT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.117&#8491;</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=6drt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6drt OCA], [http://pdbe.org/6drt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6drt RCSB], [http://www.ebi.ac.uk/pdbsum/6drt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6drt ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=6drt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6drt OCA], [https://pdbe.org/6drt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6drt RCSB], [https://www.ebi.ac.uk/pdbsum/6drt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6drt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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. [[http://www.uniprot.org/uniprot/DNLI_BPT4 DNLI_BPT4]] DNA ligase, which is expressed in the early stage of lytic development, has been implicated in T4 DNA synthesis and genetic recombination. It may also play a role in T4 DNA repair.
+[https://www.uniprot.org/uniprot/CLAMP_BPT4 CLAMP_BPT4] Sliding clamp that encircles the genomic DNA and links the DNA polymerase to the template to control the processivity of DNA synthesis. Responsible for tethering the catalytic subunit of DNA polymerase to DNA during high-speed replication (PubMed:10535942). Interaction with the sliding-clamp-loader opens the sliding clamp so that it can be loaded around the DNA template (PubMed:22194570). During transcription, encircles the DNA and tethers host RNA polymerase (RNAP) to it (PubMed:33602900).[HAMAP-Rule:MF_04161]<ref>PMID:10535942</ref> <ref>PMID:22194570</ref> <ref>PMID:33602900</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6drt" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aihara, H]]
+[[Category: Escherichia virus T4]]
-[[Category: Shi, K]]
+[[Category: Large Structures]]
-[[Category: Gene regulation]]
+[[Category: Aihara H]]
-[[Category: Hydrolase]]
+[[Category: Shi K]]
-[[Category: Processivity clamp]]

6drt

From Proteopedia

Current revision

Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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