This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1je5

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:45, 17 January 2018

Crystal Structure of gp2.5, a Single-Stranded DNA Binding Protein Encoded by Bacteriophage T7

Structural highlights

1je5 is a 2 chain structure with sequence from Bpt7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DNBI_BPT7] Single-stranded DNA-binding protein that eliminates secondary structure in long ssDNA formed on the lagging strand of the replication fork. Stimulates DNA polymerase activity and increases the efficiency of RNA primer synthesis by interacting with the DNA polymerase and the helicase/primase protein gp4. Disrupts loops, hairpins and other secondary structures present on ssDNA to reduce and eliminate pausing of viral DNA polymerase at specific sites during elongation.^[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

The gene 2.5 protein (gp2.5) of bacteriophage T7 is a single-stranded DNA (ssDNA) binding protein that has essential roles in DNA replication and recombination. In addition to binding DNA, gp2.5 physically interacts with T7 DNA polymerase and T7 primase-helicase during replication to coordinate events at the replication fork. We have determined a 1.9-A crystal structure of gp2.5 and show that it has a conserved OB-fold (oligosaccharide/oligonucleotide binding fold) that is well adapted for interactions with ssDNA. Superposition of the OB-folds of gp2.5 and other ssDNA binding proteins reveals a conserved patch of aromatic residues that stack against the bases of ssDNA in the other crystal structures, suggesting that gp2.5 binds to ssDNA in a similar manner. An acidic C-terminal extension of the gp2.5 protein, which is required for dimer formation and for interactions with the T7 DNA polymerase and the primase-helicase, appears to be flexible and may act as a switch that modulates the DNA binding affinity of gp2.5.

Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7.,Hollis T, Stattel JM, Walther DS, Richardson CC, Ellenberger T Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9557-62. Epub 2001 Jul 31. PMID:11481454^[4]

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

References

↑ Kim YT, Tabor S, Bortner C, Griffith JD, Richardson CC. Purification and characterization of the bacteriophage T7 gene 2.5 protein. A single-stranded DNA-binding protein. J Biol Chem. 1992 Jul 25;267(21):15022-31. PMID:1634538
↑ Marintcheva B, Hamdan SM, Lee SJ, Richardson CC. Essential residues in the C terminus of the bacteriophage T7 gene 2.5 single-stranded DNA-binding protein. J Biol Chem. 2006 Sep 1;281(35):25831-40. Epub 2006 Jun 28. PMID:16807232 doi:http://dx.doi.org/10.1074/jbc.M604601200
↑ Kim YT, Richardson CC. Acidic carboxyl-terminal domain of gene 2.5 protein of bacteriophage T7 is essential for protein-protein interactions. J Biol Chem. 1994 Feb 18;269(7):5270-8. PMID:8106511
↑ Hollis T, Stattel JM, Walther DS, Richardson CC, Ellenberger T. Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9557-62. Epub 2001 Jul 31. PMID:11481454 doi:10.1073/pnas.171317698

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1je5"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of gp2.5, a Single-Stranded DNA Binding Protein Encoded by Bacteriophage T7==
 <StructureSection load='1je5' size='340' side='right' caption='[[1je5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[1je5]] is a 2 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=1JE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JE5 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1je5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1je5 OCA], [http://pdbe.org/1je5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1je5 RCSB], [http://www.ebi.ac.uk/pdbsum/1je5 PDBsum]</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=1je5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1je5 OCA], [http://pdbe.org/1je5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1je5 RCSB], [http://www.ebi.ac.uk/pdbsum/1je5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1je5 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/je/1je5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/je/1je5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 27: / Line 28: @@
 </div>
 <div class="pdbe-citations 1je5" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Single-stranded DNA-binding protein|Single-stranded DNA-binding protein]]
 == References ==
 <references/>

1je5

From Proteopedia

Revision as of 08:45, 17 January 2018

Crystal Structure of gp2.5, a Single-Stranded DNA Binding Protein Encoded by Bacteriophage T7

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox