3pvv

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Current revision (10:43, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3pvv' size='340' side='right'caption='[[3pvv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3pvv' size='340' side='right'caption='[[3pvv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3pvv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PVV FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3pvv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PVV FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pvp|3pvp]]</div></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaA, MRA_0001, Rv0001 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvv OCA], [https://pdbe.org/3pvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pvv RCSB], [https://www.ebi.ac.uk/pdbsum/3pvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvv ProSAT]</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=3pvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pvv OCA], [https://pdbe.org/3pvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pvv RCSB], [https://www.ebi.ac.uk/pdbsum/3pvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pvv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/DNAA_MYCTA DNAA_MYCTA]] Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids.[HAMAP-Rule:MF_00377]
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[https://www.uniprot.org/uniprot/DNAA_MYCTA DNAA_MYCTA] Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids.[HAMAP-Rule:MF_00377]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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An essential protein, DnaA, binds to 9-bp DNA sites within the origin of replication oriC. These binding events are prerequisite to forming an enigmatic nucleoprotein scaffold that initiates replication. The number, sequences, positions, and orientations of these short DNA sites, or DnaA boxes, within the oriCs of different bacteria vary considerably. To investigate features of DnaA boxes that are important for binding Mycobacterium tuberculosis DnaA (MtDnaA), we have determined the crystal structures of the DNA binding domain (DBD) of MtDnaA bound to a cognate MtDnaA-box (at 2.0 A resolution) and to a consensus Escherichia coli DnaA-box (at 2.3 A). These structures, complemented by calorimetric equilibrium binding studies of MtDnaA DBD in a series of DnaA-box variants, reveal the main determinants of DNA recognition and establish the [T/C][T/A][G/A]TCCACA sequence as a high-affinity MtDnaA-box. Bioinformatic and calorimetric analyses indicate that DnaA-box sequences in mycobacterial oriCs generally differ from the optimal binding sequence. This sequence variation occurs commonly at the first 2 bp, making an in vivo mycobacterial DnaA-box effectively a 7-mer and not a 9-mer. We demonstrate that the decrease in the affinity of these MtDnaA-box variants for MtDnaA DBD relative to that of the highest-affinity box TTGTCCACA is less than 10-fold. The understanding of DnaA-box recognition by MtDnaA and E. coli DnaA enables one to map DnaA-box sequences in the genomes of M. tuberculosis and other eubacteria.
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Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA.,Tsodikov OV, Biswas T J Mol Biol. 2011 May 18. PMID:21620858<ref>PMID:21620858</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3pvv" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[DnaA|DnaA]]
*[[DnaA|DnaA]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Mycta]]
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[[Category: Mycobacterium tuberculosis H37Ra]]
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[[Category: Biswas, T]]
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[[Category: Biswas T]]
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[[Category: Tsodikov, O V]]
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[[Category: Tsodikov OV]]
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[[Category: Dna binding protein-dna complex]]
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[[Category: Dnaa-box]]
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[[Category: Helix-turn-helix motif]]
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[[Category: Interacting with dnaa-box]]
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Current revision

Structure of Mycobacterium tuberculosis DnaA-DBD in complex with box1 DNA

PDB ID 3pvv

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