1lrr

From Proteopedia

(Difference between revisions)

Revision as of 08:06, 31 January 2018

CRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA

Structural highlights

1lrr is a 6 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:	seqA ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SEQA_ECOLI] Negative regulator of replication initiation, which contributes to regulation of DNA replication and ensures that replication initiation occurs exactly once per chromosome per cell cycle. Binds to pairs of hemimethylated GATC sequences in the oriC region, thus preventing assembly of replication proteins and re-initiation at newly replicated origins. Repression is relieved when the region becomes fully methylated. Can also bind to hemimethylated GATC sequences outside of oriC region. Binds, with less affinity, to fully methylated GATC sites and affects timing of replication. May play a role in chromosome organization and gene regulation.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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 SeqA protein binds clusters of fully methylated or hemimethylated GATC sequences at oriC and negatively modulates the initiation of DNA replication. We find that SeqA can be proteolytically cleaved into an N-terminal multimerization and a C-terminal DNA-binding domain and have determined the crystal structure of the C-terminal domain in complex with a hemimethylated GATC site. SeqA makes direct hydrogen bonds and van der Waals contacts with the hemimethylated A-T base pair in addition to interactions with the surrounding bases and DNA backbone. The tetrameric protein-DNA complex found in the crystal suggests that SeqA binds multiple GATC sites on separate DNA duplexes, altering the overall DNA topology and sequestering oriC from replication initiation.

Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex.,Guarne A, Zhao Q, Ghirlando R, Yang W Nat Struct Biol. 2002 Nov;9(11):839-43. PMID:12379844^[7]

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

References

↑ Lu M, Campbell JL, Boye E, Kleckner N. SeqA: a negative modulator of replication initiation in E. coli. Cell. 1994 May 6;77(3):413-26. PMID:8011018
↑ von Freiesleben U, Rasmussen KV, Schaechter M. SeqA limits DnaA activity in replication from oriC in Escherichia coli. Mol Microbiol. 1994 Nov;14(4):763-72. PMID:7891562
↑ Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell. 1995 Sep 22;82(6):927-36. PMID:7553853
↑ Brendler T, Sawitzke J, Sergueev K, Austin S. A case for sliding SeqA tracts at anchored replication forks during Escherichia coli chromosome replication and segregation. EMBO J. 2000 Nov 15;19(22):6249-58. PMID:11080170 doi:10.1093/emboj/19.22.6249
↑ Skarstad K, Lueder G, Lurz R, Speck C, Messer W. The Escherichia coli SeqA protein binds specifically and co-operatively to two sites in hemimethylated and fully methylated oriC. Mol Microbiol. 2000 Jun;36(6):1319-26. PMID:10931282
↑ Sanchez-Romero MA, Busby SJ, Dyer NP, Ott S, Millard AD, Grainger DC. Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. MBio. 2010 May 18;1(1). pii: e00012-10. doi: 10.1128/mBio.00012-10. PMID:20689753 doi:10.1128/mBio.00012-10
↑ Guarne A, Zhao Q, Ghirlando R, Yang W. Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex. Nat Struct Biol. 2002 Nov;9(11):839-43. PMID:12379844 doi:http://dx.doi.org/10.1038/nsb857

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/1lrr"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA==
 <StructureSection load='1lrr' size='340' side='right' caption='[[1lrr]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">seqA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrr OCA], [http://pdbe.org/1lrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lrr RCSB], [http://www.ebi.ac.uk/pdbsum/1lrr 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=1lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrr OCA], [http://pdbe.org/1lrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lrr RCSB], [http://www.ebi.ac.uk/pdbsum/1lrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrr ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lrr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lrr_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1lrr

From Proteopedia

Revision as of 08:06, 31 January 2018

CRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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