1iu3

From Proteopedia

(Difference between revisions)

Current revision

CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH HEMIMETHYLATED DNA

Structural highlights

1iu3 is a 6 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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 Escherichia coli SeqA protein recognizes the 11 hemimethylated G-mA-T-C sites in the oriC region of the chromosome, and prevents replication over-initiation within one cell cycle. The crystal structure of the SeqA C-terminal domain with hemimethylated DNA revealed the N6-methyladenine recognition mechanism; however, the mechanism of discrimination between the hemimethylated and fully methylated states has remained elusive. In the present study, we performed mutational analyses of hemimethylated G-mA-T-C sequences with the minimal DNA-binding domain of SeqA (SeqA71-181), and found that SeqA71-181 specifically binds to hemimethylated DNA containing a sequence with a mismatched mA:G base pair [G-mA(:G)-T-C] as efficiently as the normal hemimethylated G-mA(:T)-T-C sequence. We determined the crystal structures of SeqA71-181 complexed with the mismatched and normal hemimethylated DNAs at 2.5 and 3.0 A resolutions, respectively, and found that the mismatched mA:G base pair and the normal mA:T base pair are recognized by SeqA in a similar manner. Furthermore, in both crystal structures, an electron density is present near the unmethylated adenine, which is only methylated in the fully methylated state. This electron density, which may be due to a water molecule or a metal ion, can exist in the hemimethylated state, but not in the fully methylated state, because of steric clash with the additional methyl group.

Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein.,Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S Nucleic Acids Res. 2004 Jan 2;32(1):82-92. Print 2004. PMID:14704346^[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
↑ Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S. Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein. Nucleic Acids Res. 2004 Jan 2;32(1):82-92. Print 2004. PMID:14704346 doi:http://dx.doi.org/10.1093/nar/gkh173

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/1iu3"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH HEMIMETHYLATED DNA==
-<StructureSection load='1iu3' size='340' side='right' caption='[[1iu3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='1iu3' size='340' side='right'caption='[[1iu3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1iu3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IU3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1iu3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IU3 FirstGlance]. <br>
-</td></tr><tr><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 Escherichia coli])</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]] 3&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iu3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1iu3 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iu3 TOPSAN]</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=1iu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iu3 OCA], [https://pdbe.org/1iu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1iu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iu3 ProSAT], [https://www.topsan.org/Proteins/RSGI/1iu3 TOPSAN]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SEQA_ECOLI 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.<ref>PMID:8011018</ref> <ref>PMID:7891562</ref> <ref>PMID:7553853</ref> <ref>PMID:11080170</ref> <ref>PMID:10931282</ref> <ref>PMID:20689753</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iu/1iu3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iu/1iu3_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <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=1iu3 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1iu3" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 29: / Line 33: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Fujikawa, N.]]
+[[Category: Large Structures]]
-[[Category: Hiraga, S.]]
+[[Category: Fujikawa N]]
-[[Category: Kurumizaka, H.]]
+[[Category: Hiraga S]]
-[[Category: Nureki, O.]]
+[[Category: Kurumizaka H]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Nureki O]]
-[[Category: Tanaka, Y.]]
+[[Category: Tanaka Y]]
-[[Category: Yamazoe, M.]]
+[[Category: Yamazoe M]]
-[[Category: Yokoyama, S.]]
+[[Category: Yokoyama S]]
-[[Category: Protein-dna complex]]
-[[Category: Recognition of hemimethylated dna]]
-[[Category: Replication inhibitor-dna complex]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]

1iu3

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN 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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