3TLQ

Crystal structure of EAL-like domain protein YdiV

Summary for 3TLQ

• Entry DOI: 10.2210/pdb3tlq/pdb
• Related: 4ES4
• Descriptor: Regulatory protein YdiV, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: anti-flhd4c2 factor, repress motility, transcription
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 55809.28

Authors

Li, B.,Li, N.,Wang, F.,Guo, L.,Liu, C.,Zhu, D.,Xu, S.,Gu, L. (deposition date: 2011-08-30, release date: 2012-09-12, Last modification date: 2024-03-20)

Primary citation

Li, B.,Li, N.,Wang, F.,Guo, L.,Huang, Y.,Liu, X.,Wei, T.,Zhu, D.,Liu, C.,Pan, H.,Xu, S.,Wang, H.W.,Gu, L.
Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility
Nucleic Acids Res., 40:11073-11085, 2012

PubMed Abstract: 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 Å and 2.9 Å 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.

PubMed: 23002140
DOI: 10.1093/nar/gks869

Experimental method

X-RAY DIFFRACTION (1.91 Å)