3upu: Difference between revisions

Latest revision as of 06:14, 17 October 2024

Crystal structure of the T4 Phage SF1B Helicase Dda

Structural highlights

3upu 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 3.299Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDA_BPT4 DNA helicase that stimulates viral DNA replication and recombination. Plays a role in T4 DNA replication initiation by selecting and activating DNA origins. Acts by dissociating and reassociating with the DNA molecule being unwound. Unwinds DNA as a monomer in a 5'-to-3' direction at a rate of 250 bp/s and can efficiently displace proteins from the DNA.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Helicases move on DNA via an ATP binding and hydrolysis mechanism coordinated by well-characterized helicase motifs. However, the translocation along single-stranded DNA (ssDNA) and the strand separation of double-stranded (dsDNA) may be loosely or tightly coupled. Dda is a phage T4 SF1B helicase with sequence homology to the Pif1 family of helicases that tightly couples translocation to strand separation. The crystal structure of the Dda-ssDNA binary complex reveals a domain referred to as the "pin" that was previously thought to remain static during strand separation. The pin contains a conserved phenylalanine that mediates a transient base-stacking interaction that is absolutely required for separation of dsDNA. The pin is secured at its tip by protein-protein interactions through an extended SH3 domain thereby creating a rigid strut. The conserved interface between the pin and the SH3 domain provides the mechanism for tight coupling of translocation to strand separation.

The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation.,He X, Byrd AK, Yun MK, Pemble CW 4th, Harrison D, Yeruva L, Dahl C, Kreuzer KN, Raney KD, White SW Structure. 2012 May 30. PMID:22658750^[4]

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

References

↑ Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor. Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14722-7. Epub 2002 Oct 31. PMID:12411580 doi:https://dx.doi.org/10.1073/pnas.232401899
↑ Brister JR. Origin activation requires both replicative and accessory helicases during T4 infection. J Mol Biol. 2008 Apr 11;377(5):1304-13. doi: 10.1016/j.jmb.2008.02.002. Epub 2008, Feb 9. PMID:18314134 doi:https://dx.doi.org/10.1016/j.jmb.2008.02.002
↑ Byrd AK, Matlock DL, Bagchi D, Aarattuthodiyil S, Harrison D, Croquette V, Raney KD. Dda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase. J Mol Biol. 2012 Jul 13;420(3):141-54. doi: 10.1016/j.jmb.2012.04.007. Epub 2012 , Apr 11. PMID:22504228 doi:https://dx.doi.org/10.1016/j.jmb.2012.04.007
↑ He X, Byrd AK, Yun MK, Pemble CW 4th, Harrison D, Yeruva L, Dahl C, Kreuzer KN, Raney KD, White SW. The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation. Structure. 2012 May 30. PMID:22658750 doi:10.1016/j.str.2012.04.013

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OCA

[1] Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor. Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14722-7. Epub 2002 Oct 31. PMID:12411580 doi:https://dx.doi.org/10.1073/pnas.232401899

[2] Brister JR. Origin activation requires both replicative and accessory helicases during T4 infection. J Mol Biol. 2008 Apr 11;377(5):1304-13. doi: 10.1016/j.jmb.2008.02.002. Epub 2008, Feb 9. PMID:18314134 doi:https://dx.doi.org/10.1016/j.jmb.2008.02.002

[3] Byrd AK, Matlock DL, Bagchi D, Aarattuthodiyil S, Harrison D, Croquette V, Raney KD. Dda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase. J Mol Biol. 2012 Jul 13;420(3):141-54. doi: 10.1016/j.jmb.2012.04.007. Epub 2012 , Apr 11. PMID:22504228 doi:https://dx.doi.org/10.1016/j.jmb.2012.04.007

[4] He X, Byrd AK, Yun MK, Pemble CW 4th, Harrison D, Yeruva L, Dahl C, Kreuzer KN, Raney KD, White SW. The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation. Structure. 2012 May 30. PMID:22658750 doi:10.1016/j.str.2012.04.013

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='3upu' size='340' side='right'caption='[[3upu]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3upu]] is a 6 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=3UPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UPU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3upu]] 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=3UPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UPU FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.299&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dda, sud ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=3upu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3upu OCA], [https://pdbe.org/3upu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3upu RCSB], [https://www.ebi.ac.uk/pdbsum/3upu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3upu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DDA_BPT4 DDA_BPT4]] DNA helicase that stimulates viral DNA replication and recombination. Plays a role in T4 DNA replication initiation by selecting and activating DNA origins. Acts by dissociating and reassociating with the DNA molecule being unwound. Unwinds DNA as a monomer in a 5'-to-3' direction at a rate of 250 bp/s and can efficiently displace proteins from the DNA.<ref>PMID:12411580</ref> <ref>PMID:18314134</ref> <ref>PMID:22504228</ref>
+[https://www.uniprot.org/uniprot/DDA_BPT4 DDA_BPT4] DNA helicase that stimulates viral DNA replication and recombination. Plays a role in T4 DNA replication initiation by selecting and activating DNA origins. Acts by dissociating and reassociating with the DNA molecule being unwound. Unwinds DNA as a monomer in a 5'-to-3' direction at a rate of 250 bp/s and can efficiently displace proteins from the DNA.<ref>PMID:12411580</ref> <ref>PMID:18314134</ref> <ref>PMID:22504228</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Bpt4]]
+[[Category: Escherichia virus T4]]
-[[Category: DNA helicase]]
 [[Category: Large Structures]]
-[[Category: He, X]]
+[[Category: He X]]
-[[Category: IV, C W.Pemble]]
+[[Category: Kreuzer KN]]
-[[Category: Kreuzer, K N]]
+[[Category: Pemble IV CW]]
-[[Category: Raney, K D]]
+[[Category: Raney KD]]
-[[Category: White, S W]]
+[[Category: White SW]]
-[[Category: Yun, M K]]
+[[Category: Yun MK]]
-[[Category: Coupling atp hydrolysis to dna unwinding]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Pin-tower interface]]
-[[Category: Reca-like domain]]
-[[Category: Sh3 domain]]
-[[Category: Ssdna]]

3upu: Difference between revisions

Latest revision as of 06:14, 17 October 2024

Crystal structure of the T4 Phage SF1B Helicase Dda

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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