Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.47 kDa 
• Atom Count: 2325 
• Residue Count: 299 
• Unique protein chains: 1

6BAR

Crystal structure of Thermus thermophilus Rod shape determining protein RodA (Q5SIX3_THET8)

• DOI: 10.2210/pdb6BAR/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-15 Released: 2018-03-28 
• Deposition Author(s): Sjodt, M., Brock, K., Dobihal, G., Rohs, P.D.A., Green, A.G., Hopf, T.A., Meeske, A.J., Marks, D.S., Bernhardt, T.G., Rudner, D.Z., Kruse, A.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.274 
• R-Value Work: 0.229 
• R-Value Observed: 0.234 

Literature

Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.

Sjodt, M., Brock, K., Dobihal, G., Rohs, P.D.A., Green, A.G., Hopf, T.A., Meeske, A.J., Srisuknimit, V., Kahne, D., Walker, S., Marks, D.S., Bernhardt, T.G., Rudner, D.Z., Kruse, A.C.

(2018) Nature 556: 118-121

• PubMed: 29590088 
• DOI: 10.1038/nature25985
• Primary Citation of Related Structures:  
  6BAR, 6BAS


• PubMed Abstract: 
  

The shape, elongation, division and sporulation (SEDS) proteins are a large family of ubiquitous and essential transmembrane enzymes with critical roles in bacterial cell wall biology. The exact function of SEDS proteins was for a long time poorly understood, but recent work has revealed that the prototypical SEDS family member RodA is a peptidoglycan polymerase-a role previously attributed exclusively to members of the penicillin-binding protein family. This discovery has made RodA and other SEDS proteins promising targets for the development of next-generation antibiotics. However, little is known regarding the molecular basis of SEDS activity, and no structural data are available for RodA or any homologue thereof. Here we report the crystal structure of Thermus thermophilus RodA at a resolution of 2.9 Å, determined using evolutionary covariance-based fold prediction to enable molecular replacement. The structure reveals a ten-pass transmembrane fold with large extracellular loops, one of which is partially disordered. The protein contains a highly conserved cavity in the transmembrane domain, reminiscent of ligand-binding sites in transmembrane receptors. Mutagenesis experiments in Bacillus subtilis and Escherichia coli show that perturbation of this cavity abolishes RodA function both in vitro and in vivo, indicating that this cavity is catalytically essential. These results provide a framework for understanding bacterial cell wall synthesis and SEDS protein function.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rod shape determining protein RodA	A	359	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1241, rodA EC: 2.4.1.129
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Shape, Elongation, Division, and Sporulation (SEDS) Proteins	Protein:  RodA peptidoglycan polymerase
Find proteins for Q5SIX3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore Q5SIX3  Go to UniProtKB:  Q5SIX3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	A	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.274 
• R-Value Work: 0.229 
• R-Value Observed: 0.234 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.405	α = 90
b = 80.012	β = 91.06
c = 47.827	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-15 
• Released Date: 2018-03-28 
Deposition Author(s): Sjodt, M., Brock, K., Dobihal, G., Rohs, P.D.A., Green, A.G., Hopf, T.A., Meeske, A.J., Marks, D.S., Bernhardt, T.G., Rudner, D.Z., Kruse, A.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI109764

Revision History 

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Data collection, Database references
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence