7R6R | pdb_00007r6r

Crystal Structure of a Mycobacteriophage Cluster A2 Immunity Repressor:DNA Complex

• PDB DOI: https://doi.org/10.2210/pdb7R6R/pdb
• NAKB: 7R6R

• Classification: GENE REGULATION/DNA
• Organism(s): Mycobacterium phage TipsytheTRex
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-23 Released: 2022-07-20 
• Deposition Author(s): McGinnis, R.J., Brambley, C.A., Stamey, B., Green, W.C., Gragg, K.N., Cafferty, E.R., Terwilliger, T.C., Hammel, M., Hollis, T.J., Miller, J.M., Gainey, M.D., Wallen, J.R.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 
  0.248 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence.

McGinnis, R.J., Brambley, C.A., Stamey, B., Green, W.C., Gragg, K.N., Cafferty, E.R., Terwilliger, T.C., Hammel, M., Hollis, T.J., Miller, J.M., Gainey, M.D., Wallen, J.R.

(2022) Nat Commun 13: 4105-4105

• PubMed: 35835745 
• DOI: https://doi.org/10.1038/s41467-022-31678-6
• Primary Citation Related Structures: 
  7R6R, 7TZ1


• PubMed Abstract: 
  

  Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.

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Organizational Affiliation: 
• Western Carolina University, Department of Chemistry and Physics, 111 Memorial Drive, Cullowhee, NC, 28723, USA.
Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
Middle Tennessee State University, Department of Chemistry, 1301 East Main Street, Murfreesboro, TN, 37132, USA.
Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
New Mexico Consortium, Los Alamos, NM, 87544, USA.
Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA.
Western Carolina University, Department of Chemistry and Physics, 111 Memorial Drive, Cullowhee, NC, 28723, USA. [e-mail].
Western Carolina University, Department of Chemistry and Physics, 111 Memorial Drive, Cullowhee, NC, 28723, USA. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 36.53 kDa 
• Atom Count: 2,256 
• Modeled Residue Count: 209 
• Deposited Residue Count: 245 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity repressor	A	203	Mycobacterium phage TipsytheTRex	Mutation(s): 0  Gene Names: SEA_TIPSYTHETREX_75
UniProt
Find proteins for Q05286 (Mycobacterium phage L5) Explore Q05286  Go to UniProtKB:  Q05286

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*CP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*CP*GP*GP*G)-3')	B	21	Mycobacterium phage TipsytheTRex

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*CP*GP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*GP*AP*AP*A)-3')	C	21	Mycobacterium phage TipsytheTRex

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.248 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.49	α = 90
b = 43.51	β = 102.257
c = 89.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): McGinnis, R.J., Brambley, C.A., Stamey, B., Green, W.C., Gragg, K.N., Cafferty, E.R., Terwilliger, T.C., Hammel, M., Hollis, T.J., Miller, J.M., Gainey, M.D., Wallen, J.R.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2022-07-27
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description