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Structure of IDP90225

Structure of a putative YscO homolog CT670 from Chlamydia trachomatis

Edit deposit information
CSGID target
IDP90225 
PDB Id
3K29 (NCBI MMDB
Authors
R.Lam,A.Singer,T.Skarina,O.Onopriyenko,A.Bochkarev,J.S.Brunzelle,A.M.Edwards,W.F.Anderson,N.Y.Chirgadze,A.Savchenko 
Responsible person
Alexander Singer 
Responsible lab
University of Calgary 
Deposition Date
Sep 29, 2009 
Release Date
Oct 13, 2009 

Annotation

Description
Gram-negative pathogens exert a much of their virulence through the secretion of toxins, termed effectors, through the type III secretion system. This involves the multi-step assembly of a nanomachine, termed the “type III secretion apparatus” (T3SA), to form a “needle” spanning the bacterial and host membranes, and through this needle, the effectors are passed from the bacteria to the host. Assembly of the T3SA is related to assembly of the bacterial flagellum, as a number of proteins involved in flagellar assembly have counterparts in the type III secretion system. The YscO family of proteins are known to be involved in assembly of the type III secretion system and is thought to be related to the flagellar protein FliJ. Its role in assembly of the type III apparatus is unclear, but has been shown to interact with the “molecular ruler” YscP which designates the needle length. In addition, both YscO and FliJ have been shown to bind type III and flagellar chaperones, respectively, following release of cargo by these chaperones. We report the structure of CT670, the homologue of YscO from Chlamydia trachomatis, to 2 Å. This is the first reported structure of a YscO or FliJ protein, and its structure is revealed to be a coiled-coil containing almost exclusively 2 very long helices over its 168 residues. The first helix is “straightened” by Pro5 at the N-terminus, and this conformation is held by the insertion of the Tyr4 ring into a hydrophobic patch in the middle of the coiled coil. Overall the resulting structure is highly elongated and predicted to be monomeric, with patches of electropositive and electronegative potential over its length. This protein has been shown to bind to its YscP homologue, CT671; the molecular mechanism for this interaction or its interaction with type III chaperones has yet to be determined. The overall structure of CT670 is an elongated coiled coil with two very large helices. Based on its crystal packing interactions, this protein is expected to be monomeric in solution. 
Functional assignment
Type III Secretion System Assembly 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=83.11Å, b=23.19Å, c=105.62Å
α=90.00, β=107.48, γ=90.00 
Solvent content
47.75  
Matthews coefficient
2.35  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
27.41-1.99Å (2.04-1.99Å)  
Rall(%)
24.2 
Rwork(%)
24.0 (27.7) 
Rfree(%)
28.5 (32.8) 
Num. observed reflections
13431 (780) 
Num. Rfree reflections
658 (41) 
Completeness(%)
98.2 (79.5) 

Model parameters

Num Atoms
1454  
Num Waters
51  
Num Hetatoms
0  
Model mean isotropic B factor
24.040Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.535°  
Filename uploaded
ct670pk_x1c2_final.pdb (uploaded on Oct 14, 2009 5:12 PM)  
Inserted
Oct 14, 2009