1c1k: Difference between revisions

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<StructureSection load='1c1k' size='340' side='right'caption='[[1c1k]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='1c1k' size='340' side='right'caption='[[1c1k]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1c1k]] is a 1 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=1C1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C1K FirstGlance]. <br>
<table><tr><td colspan='2'>[[1c1k]] is a 1 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=1C1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C1K FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IR:IRIDIUM+ION'>IR</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]] 1.45&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IR:IRIDIUM+ION'>IR</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=1c1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1k OCA], [https://pdbe.org/1c1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c1k RCSB], [https://www.ebi.ac.uk/pdbsum/1c1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1k 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=1c1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1k OCA], [https://pdbe.org/1c1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c1k RCSB], [https://www.ebi.ac.uk/pdbsum/1c1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1k ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/VG59_BPT4 VG59_BPT4]] DNA-binding protein involved in genetic recombination and recombination-dependent DNA replication. It forms a protein complex with the gene 41 protein that partly replaces the dDA protein helicase function. It has higher affinity for single- than for double-stranded DNA. It can bind directly protein 32.  
[https://www.uniprot.org/uniprot/HLOAD_BPT4 HLOAD_BPT4] DNA helicase loader protein that participates in viral DNA replication, recombination, and repair (PubMed:10871615). At the fork, required for loading of the replicative helicase onto DNA protected by the ssDNA-binding protein (PubMed:11459967, PubMed:7806533, PubMed:10871615, PubMed:22427673). Coordinates simultaneous synthesis of leading- and lagging-strands (PubMed:11459969).[HAMAP-Rule:MF_04156]<ref>PMID:10871615</ref> <ref>PMID:11459967</ref> <ref>PMID:22427673</ref> <ref>PMID:7806533</ref> <ref>PMID:11459969</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1c1k 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=1c1k ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The bacteriophage T4 gene 59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene 59 helicase assembly protein accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene 59 helicase assembly protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA. We show here that T4 gene 59 helicase assembly protein binds most tightly to fork DNA substrates, with either single or almost entirely double-stranded arms. Our studies suggest that the helicase assembly protein is responsible for loading T4 gene 41 helicase specifically at replication forks, and that its binding sites for each arm must hold more than six, but not more than 12 nucleotides. The 1.45 A resolution crystal structure of the full-length 217-residue monomeric T4 gene 59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules. The N-terminal domain has structural similarity to the double-stranded DNA binding domain of rat HMG1A. We propose a speculative model of how the T4 gene 59 helicase assembly protein might bind to fork DNA based on the similarity to HMG1, the location of the basic and hydrophobic regions, and the site size of the fork arms needed for tight fork DNA binding. The fork-binding model suggests putative binding sites for the T4 gene 32 single-stranded DNA binding protein and for the hexameric T4 gene 41 helicase assembly.
Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold.,Mueser TC, Jones CE, Nossal NG, Hyde CC J Mol Biol. 2000 Feb 18;296(2):597-612. PMID:10669611<ref>PMID:10669611</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1c1k" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bpt4]]
[[Category: Escherichia virus T4]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hyde, C C]]
[[Category: Hyde CC]]
[[Category: Jones, C E]]
[[Category: Jones CE]]
[[Category: Mueser, T C]]
[[Category: Mueser TC]]
[[Category: Nossal, N G]]
[[Category: Nossal NG]]
[[Category: Dna binding protein]]
[[Category: Dna recombination]]
[[Category: Dna replication]]
[[Category: Forked dna]]
[[Category: Helicase assembly]]

Latest revision as of 09:40, 7 February 2024

BACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEINBACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEIN

Structural highlights

1c1k is a 1 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 1.45Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HLOAD_BPT4 DNA helicase loader protein that participates in viral DNA replication, recombination, and repair (PubMed:10871615). At the fork, required for loading of the replicative helicase onto DNA protected by the ssDNA-binding protein (PubMed:11459967, PubMed:7806533, PubMed:10871615, PubMed:22427673). Coordinates simultaneous synthesis of leading- and lagging-strands (PubMed:11459969).[HAMAP-Rule:MF_04156][1] [2] [3] [4] [5]

Evolutionary Conservation

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

References

  1. ↑ Jones CE, Mueser TC, Nossal NG. Interaction of the bacteriophage T4 gene 59 helicase loading protein and gene 41 helicase with each other and with fork, flap, and cruciform DNA. J Biol Chem. 2000 Sep 1;275(35):27145-54. PMID:10871615 doi:10.1074/jbc.M003808200
  2. ↑ Bleuit JS, Xu H, Ma Y, Wang T, Liu J, Morrical SW. Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNA replication and repair. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8298-305. PMID:11459967 doi:10.1073/pnas.131007498
  3. ↑ Dolezal D, Jones CE, Lai X, Brister JR, Mueser TC, Nossal NG, Hinton DM. Mutational analysis of the T4 gp59 helicase loader reveals its sites for interaction with helicase, single-stranded binding protein, and DNA. J Biol Chem. 2012 May 25;287(22):18596-607. PMID:22427673 doi:10.1074/jbc.M111.332080
  4. ↑ Barry J, Alberts B. Purification and characterization of bacteriophage T4 gene 59 protein. A DNA helicase assembly protein involved in DNA replication. J Biol Chem. 1994 Dec 30;269(52):33049-62 PMID:7806533
  5. ↑ Jones CE, Mueser TC, Dudas KC, Kreuzer KN, Nossal NG. Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: a versatile couple with roles in replication and recombination. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8312-8. PMID:11459969 doi:10.1073/pnas.121009398

1c1k, resolution 1.45Å

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