1e0j: Difference between revisions

Revision as of 04:15, 30 August 2017

gp4d helicase from phage T7 ADPNP complex

Structural highlights

1e0j is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ANP, MG
Related:	1e0k, 1b79, 1jwe, 1cr0, 1cr1, 1cr2, 1cr4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PRIM_BPT7] Synthesizes short RNA primers for DNA replication. Unwinds the DNA at the replication forks and generates single-stranded DNA for both leading and lagging strand synthesis. The primase synthesizes short RNA primers on the lagging strand that the polymerase elongates using dNTPs.^[1] ^[2] ^[3]

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

We have determined the crystal structure of an active, hexameric fragment of the gene 4 helicase from bacteriophage T7. The structure reveals how subunit contacts stabilize the hexamer. Deviation from expected six-fold symmetry of the hexamer indicates that the structure is of an intermediate on the catalytic pathway. The structural consequences of the asymmetry suggest a "binding change" mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled to conformational changes in the ring that most likely accompany duplex unwinding. The structure of a complex with a nonhydrolyzable ATP analog provides additional evidence for this hypothesis, with only four of the six possible nucleotide binding sites being occupied in this conformation of the hexamer. This model suggests a mechanism for DNA translocation.

Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.,Singleton MR, Sawaya MR, Ellenberger T, Wigley DB Cell. 2000 Jun 9;101(6):589-600. PMID:10892646^[4]

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

References

↑ Kong D, Griffith JD, Richardson CC. Gene 4 helicase of bacteriophage T7 mediates strand transfer through pyrimidine dimers, mismatches, and nonhomologous regions. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2987-92. PMID:9096333
↑ Zhang H, Lee SJ, Zhu B, Tran NQ, Tabor S, Richardson CC. Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis. Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9372-7. doi:, 10.1073/pnas.1106678108. Epub 2011 May 23. PMID:21606333 doi:https://dx.doi.org/10.1073/pnas.1106678108
↑ Kulczyk AW, Akabayov B, Lee SJ, Bostina M, Berkowitz SA, Richardson CC. An interaction between DNA polymerase and helicase is essential for the high processivity of the bacteriophage T7 replisome. J Biol Chem. 2012 Nov 9;287(46):39050-60. doi: 10.1074/jbc.M112.410647. Epub 2012, Sep 12. PMID:22977246 doi:https://dx.doi.org/10.1074/jbc.M112.410647
↑ Singleton MR, Sawaya MR, Ellenberger T, Wigley DB. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell. 2000 Jun 9;101(6):589-600. PMID:10892646

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kong D, Griffith JD, Richardson CC. Gene 4 helicase of bacteriophage T7 mediates strand transfer through pyrimidine dimers, mismatches, and nonhomologous regions. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2987-92. PMID:9096333

[2] Zhang H, Lee SJ, Zhu B, Tran NQ, Tabor S, Richardson CC. Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis. Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9372-7. doi:, 10.1073/pnas.1106678108. Epub 2011 May 23. PMID:21606333 doi:https://dx.doi.org/10.1073/pnas.1106678108

[3] Kulczyk AW, Akabayov B, Lee SJ, Bostina M, Berkowitz SA, Richardson CC. An interaction between DNA polymerase and helicase is essential for the high processivity of the bacteriophage T7 replisome. J Biol Chem. 2012 Nov 9;287(46):39050-60. doi: 10.1074/jbc.M112.410647. Epub 2012, Sep 12. PMID:22977246 doi:https://dx.doi.org/10.1074/jbc.M112.410647

[4] Singleton MR, Sawaya MR, Ellenberger T, Wigley DB. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell. 2000 Jun 9;101(6):589-600. PMID:10892646

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@@ Line 1: / Line 1: @@
-==GP4D HELICASE FROM PHAGE T7 ADPNP COMPLEX==
+==gp4d helicase from phage T7 ADPNP complex==
 <StructureSection load='1e0j' size='340' side='right' caption='[[1e0j]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1e0j]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1e0j]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0J FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1e0k|1e0k]], [[1b79|1b79]], [[1jwe|1jwe]], [[1cr0|1cr0]], [[1cr1|1cr1]], [[1cr2|1cr2]], [[1cr4|1cr4]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GENE 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</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=1e0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0j OCA], [http://pdbe.org/1e0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0j RCSB], [http://www.ebi.ac.uk/pdbsum/1e0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0j ProSAT]</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=1e0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0j OCA], [http://pdbe.org/1e0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0j RCSB], [http://www.ebi.ac.uk/pdbsum/1e0j PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 18: @@
      <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=1e0j ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bpt7]]
 [[Category: Ellenberger, T]]
 [[Category: Sawaya, M R]]

1e0j: Difference between revisions

Revision as of 04:15, 30 August 2017

gp4d helicase from phage T7 ADPNP complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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