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4es4

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Crystal structure of YdiV and FlhD complex

Structural highlights

4es4 is a 8 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YDIV_ECOLI Upon overexpression acts as a novel anti-FlhC(2)FlhD(4) factor, decreasing its DNA-binding activity, able to negatively regulate expression of flagellar class II operons including FliC.^[1]

Publication Abstract from PubMed

YdiV is a negative regulator of cell motility. It interacts with FlhD(4)C(2) complex, a product of flagellar master operon, which works as the transcription activator of all other flagellar operons. Here, we report the crystal structures of YdiV and YdiV(2)-FlhD(2) complex at 1.9 A and 2.9 A resolutions, respectively. Interestingly, YdiV formed multiple types of complexes with FlhD(4)C(2). YdiV(1)-FlhD(4)C(2) and YdiV(2)-FlhD(4)C(2) still bound to DNA, while YdiV(3)-FlhD(4)C(2) and YdiV(4)-FlhD(4)C(2) did not. DNA bound FlhD(4)C(2) through wrapping around the FlhC subunit rather than the FlhD subunit. Structural analysis showed that only two peripheral FlhD subunits were accessible for YdiV binding, forming the YdiV(2)-FlhD(4)C(2) complex without affecting the integrity of ring-like structure. YdiV(2)-FlhD(2) structure and the negative staining electron microscopy reconstruction of YdiV(4)-FlhD(4)C(2) suggested that the third and fourth YdiV molecule bound to the FlhD(4)C(2) complex through squeezing into the ring-like structure of FlhD(4)C(2) between the two internal D subunits. Consequently, the ring-like structure opened up, and the complex lost DNA-binding ability. Thus, YdiV inhibits FlhD(4)C(2) only at relatively high concentrations.

Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility.,Li B, Li N, Wang F, Guo L, Huang Y, Liu X, Wei T, Zhu D, Liu C, Pan H, Xu S, Wang HW, Gu L Nucleic Acids Res. 2012 Sep 21. PMID:23002140^[2]

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

References

↑ Wada T, Hatamoto Y, Kutsukake K. Functional and expressional analyses of the anti-FlhD4C2 factor gene ydiV in Escherichia coli. Microbiology. 2012 Jun;158(Pt 6):1533-42. doi: 10.1099/mic.0.056036-0. Epub 2012 , Mar 29. PMID:22461489 doi:http://dx.doi.org/10.1099/mic.0.056036-0
↑ Li B, Li N, Wang F, Guo L, Huang Y, Liu X, Wei T, Zhu D, Liu C, Pan H, Xu S, Wang HW, Gu L. Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility. Nucleic Acids Res. 2012 Sep 21. PMID:23002140 doi:10.1093/nar/gks869

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/4es4"

Categories: Escherichia coli K-12 | Large Structures | Gu L | Li B

@@ Line 1: / Line 1: @@
 ==Crystal structure of YdiV and FlhD complex==
-<StructureSection load='4es4' size='340' side='right' caption='[[4es4]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='4es4' size='340' side='right'caption='[[4es4]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4es4]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ES4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ES4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4es4]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ES4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ES4 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3tlq|3tlq]]</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]] 2.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cdgR, ydiV, b1707, JW1697 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), flhD, flbB, b1892, JW1881 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=4es4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4es4 OCA], [https://pdbe.org/4es4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4es4 RCSB], [https://www.ebi.ac.uk/pdbsum/4es4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4es4 ProSAT]</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=4es4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4es4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4es4 RCSB], [http://www.ebi.ac.uk/pdbsum/4es4 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/YDIV_ECOLI YDIV_ECOLI] Upon overexpression acts as a novel anti-FlhC(2)FlhD(4) factor, decreasing its DNA-binding activity, able to negatively regulate expression of flagellar class II operons including FliC.<ref>PMID:22461489</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 17: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4es4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli k-12]]
+[[Category: Escherichia coli K-12]]
-[[Category: Gu, L]]
+[[Category: Large Structures]]
-[[Category: Li, B]]
+[[Category: Gu L]]
-[[Category: Flagellar regulation]]
+[[Category: Li B]]
-[[Category: Transcription]]

4es4

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Current revision

Crystal structure of YdiV and FlhD complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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