4itq

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of hypothetical protein SCO1480 bound to DNA

Structural highlights

4itq is a 3 chain structure with sequence from Streptomyces coelicolor A3(2). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IHF_STRCO A nucleoid-associated protein (NAP) that probably plays a role in chromosome compactation. Contributes to development and secondary metabolism, but is dispensable for growth and viability (PubMed:22038127, PubMed:23427309). Binds to the promoter region of a number of genes (including itself); multiple molecules of the protein bind to the DNA simultaneously, deletion alters the expression of about 30 genes (both up- and down-regulation occurs). Plays a role in controlling viability (PubMed:22038127). Binds dsDNA without any obvious sequence specificity, in a concentration and length-dependent manner. Promotes supercoiling in a topoisomerase-dependent manner (counteracts TopA plasmid relaxation). Binds DNA as a monomer, contacting 8 base pairs via the phosphate backbone; each monomer can bind 2 DNA duplexes, allowing a bridging function (PubMed:23427309). Alters DNA topology, constraining negative supercoils, possibly by DNA twist. Longer dsDNA binds more than one sIHF subunit (PubMed:31376411).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Effective chromosome organization is central to the functioning of any cell. In bacteria, this organization is achieved through the concerted activity of multiple nucleoid-associated proteins. These proteins are not, however, universally conserved, and different groups of bacteria have distinct subsets that contribute to chromosome architecture. Here, we describe the characterization of a novel actinobacterial-specific protein in Streptomyces coelicolor. We show that sIHF (SCO1480) associates with the nucleoid and makes important contributions to chromosome condensation and chromosome segregation during Streptomyces sporulation. It also affects antibiotic production, suggesting an additional role in gene regulation. In vitro, sIHF binds DNA in a length-dependent but sequence-independent manner, without any obvious structural preferences. It does, however, impact the activity of topoisomerase, significantly altering DNA topology. The sIHF-DNA co-crystal structure reveals sIHF to be composed of two domains: a long N-terminal helix and a C-terminal helix-two turns-helix domain with two separate DNA interaction sites, suggesting a potential role in bridging DNA molecules.

A novel nucleoid-associated protein specific to the actinobacteria.,Swiercz JP, Nanji T, Gloyd M, Guarne A, Elliot MA Nucleic Acids Res. 2013 Feb 20. PMID:23427309^[4]

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

References

↑ Yang YH, Song E, Willemse J, Park SH, Kim WS, Kim EJ, Lee BR, Kim JN, van Wezel GP, Kim BG. A novel function of Streptomyces integration host factor (sIHF) in the control of antibiotic production and sporulation in Streptomyces coelicolor. Antonie Van Leeuwenhoek. 2012 Mar;101(3):479-92. PMID:22038127 doi:10.1007/s10482-011-9657-z
↑ Swiercz JP, Nanji T, Gloyd M, Guarne A, Elliot MA. A novel nucleoid-associated protein specific to the actinobacteria. Nucleic Acids Res. 2013 Feb 20. PMID:23427309 doi:10.1093/nar/gkt095
↑ Nanji T, Gehrke EJ, Shen Y, Gloyd M, Zhang X, Firby CD, Huynh A, Razi A, Ortega J, Elliot MA, Guarne A. Streptomyces IHF uses multiple interfaces to bind DNA. Biochim Biophys Acta Gen Subj. 2019 Nov;1863(11):129405. doi:, 10.1016/j.bbagen.2019.07.014. Epub 2019 Jul 31. PMID:31376411 doi:http://dx.doi.org/10.1016/j.bbagen.2019.07.014
↑ Swiercz JP, Nanji T, Gloyd M, Guarne A, Elliot MA. A novel nucleoid-associated protein specific to the actinobacteria. Nucleic Acids Res. 2013 Feb 20. PMID:23427309 doi:10.1093/nar/gkt095

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4itq"

@@ Line 1: / Line 1: @@
 ==Crystal structure of hypothetical protein SCO1480 bound to DNA==
-<StructureSection load='4itq' size='340' side='right' caption='[[4itq]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='4itq' size='340' side='right'caption='[[4itq]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4itq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ITQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ITQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4itq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ITQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ITQ FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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]] 2.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCO1480 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4itq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4itq OCA], [http://pdbe.org/4itq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4itq RCSB], [http://www.ebi.ac.uk/pdbsum/4itq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4itq 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=4itq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4itq OCA], [https://pdbe.org/4itq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4itq RCSB], [https://www.ebi.ac.uk/pdbsum/4itq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4itq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/IHF_STRCO IHF_STRCO] A nucleoid-associated protein (NAP) that probably plays a role in chromosome compactation. Contributes to development and secondary metabolism, but is dispensable for growth and viability (PubMed:22038127, PubMed:23427309). Binds to the promoter region of a number of genes (including itself); multiple molecules of the protein bind to the DNA simultaneously, deletion alters the expression of about 30 genes (both up- and down-regulation occurs). Plays a role in controlling viability (PubMed:22038127). Binds dsDNA without any obvious sequence specificity, in a concentration and length-dependent manner. Promotes supercoiling in a topoisomerase-dependent manner (counteracts TopA plasmid relaxation). Binds DNA as a monomer, contacting 8 base pairs via the phosphate backbone; each monomer can bind 2 DNA duplexes, allowing a bridging function (PubMed:23427309). Alters DNA topology, constraining negative supercoils, possibly by DNA twist. Longer dsDNA binds more than one sIHF subunit (PubMed:31376411).<ref>PMID:22038127</ref> <ref>PMID:23427309</ref> <ref>PMID:31376411</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Strco]]
+[[Category: Large Structures]]
-[[Category: Elliot, M A]]
+[[Category: Elliot MA]]
-[[Category: Gloyd, M]]
+[[Category: Gloyd M]]
-[[Category: Guarne, A]]
+[[Category: Guarne A]]
-[[Category: Nanji, T]]
+[[Category: Nanji T]]
-[[Category: Swiercz, J P]]
+[[Category: Swiercz JP]]
-[[Category: Gene regulation]]
-[[Category: H2th motif]]
-[[Category: Nucleoid-associated protein]]
-[[Category: Protein-dna complex]]
-[[Category: Structural protein-dna complex]]

4itq

From Proteopedia

Current revision

Crystal structure of hypothetical protein SCO1480 bound to DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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