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.

1ka8

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 05:03, 11 September 2015

Crystal Structure of the Phage P4 Origin-Binding Domain

Structural highlights

1ka8 is a 6 chain structure with sequence from Bpp4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[PRIM_BPP4] This protein acts as a DNA primase generating di- to pentaribonucleotides; the predominant product being the dimer pppApG. It complexes specifically to the P4 origin of replication (ori) and its cis replication region (crr). It also acts as a DNA helicase.

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 origin-binding domain of the gpalpha protein of phage P4 (P4-OBD) mediates origin recognition and regulation of gpalpha activity by the protein Cnr. We have determined the crystal structure of P4-OBD at 2.95 A resolution. The structure of P4-OBD is that of a dimer with pseudo twofold symmetry. Each subunit has a winged helix topology with a unique structure among initiator proteins. The only structural homologue of the P4-OBD subunit is the DNA-binding domain of the eukaryotic transcriptional activator Rfx1. Based on this structural alignment, a model for origin recognition by the P4-OBD dimer is suggested. P4-OBD mutations that interfere with Cnr binding locate to the dimer interface, indicating that Cnr acts by disrupting the gpalpha dimer. P4-OBD dimerization is mediated by helices alpha1 and alpha3 in both subunits, a mode of winged helix protein dimerization that is reminiscent of that of the eukaryotic transcription factors E2F and DP. This, in turn, suggests that Cnr is also a winged helix protein, a possibility that is supported by previously unreported sequence homologies between Cnr and Rfx1 and homology modelling. Hence, in a mechanism that appears to be conserved from phage to man, the DNA-binding activity of winged helix proteins can be regulated by other winged helix proteins via the versatile use of the winged helix motif as a homo- or heterodimerization scaffold.

Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteins.,Yeo HJ, Ziegelin G, Korolev S, Calendar R, Lanka E, Waksman G Mol Microbiol. 2002 Feb;43(4):855-67. PMID:11929537^[1]

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

References

↑ Yeo HJ, Ziegelin G, Korolev S, Calendar R, Lanka E, Waksman G. Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteins. Mol Microbiol. 2002 Feb;43(4):855-67. PMID:11929537

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/1ka8"

@@ Line 2: / Line 2: @@
 <StructureSection load='1ka8' size='340' side='right' caption='[[1ka8]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ka8]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p4 Enterobacteria phage p4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KA8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ka8]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp4 Bpp4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KA8 FirstGlance]. <br>
-</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=1ka8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ka8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ka8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ka8 PDBsum]</span></td></tr>
+</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=1ka8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ka8 OCA], [http://pdbe.org/1ka8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ka8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ka8 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 25: / Line 25: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ka8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Enterobacteria phage p4]]
+[[Category: Bpp4]]
 [[Category: Calendar, R]]
 [[Category: Korolev, S]]

1ka8

From Proteopedia

Revision as of 05:03, 11 September 2015

Crystal Structure of the Phage P4 Origin-Binding Domain

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