Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.50 kDa 
• Atom Count: 4866 
• Residue Count: 522 
• Unique protein chains: 1

5CAJ

Crystal structure of E. coli YaaA, a member of the DUF328/UPF0246 family

• DOI: 10.2210/pdb5CAJ/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-29 Released: 2016-02-24 
• Deposition Author(s): Prahlad, J., Lin, J., Wilson, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.176 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Literature

The DUF328 family member YaaA is a DNA-binding protein with a novel fold.

Prahlad, J., Yuan, Y., Lin, J., Chang, C.W., Iwata-Reuyl, D., Liu, Y., de Crecy-Lagard, V., Wilson, M.A.

(2020) J Biol Chem 295: 14236-14247

• PubMed: 32796037 
• DOI: 10.1074/jbc.RA120.015055
• Primary Citation of Related Structures:  
  5CAJ


• PubMed Abstract: 
  

DUF328 family proteins are present in many prokaryotes; however, their molecular activities are unknown. The Escherichia coli DUF328 protein YaaA is a member of the OxyR regulon and is protective against oxidative stress. Because uncharacterized proteins involved in prokaryotic oxidative stress response are rare, we sought to learn more about the DUF328 family. Using comparative genomics, we found a robust association between the DUF328 family and genes involved in DNA recombination and the oxidative stress response. In some proteins, DUF328 domains are fused to other domains involved in DNA binding, recombination, and repair. Cofitness analysis indicates that DUF328 family genes associate with recombination-mediated DNA repair pathways, particularly the RecFOR pathway. Purified recombinant YaaA binds to dsDNA, duplex DNA containing bubbles of unpaired nucleotides, and Holliday junction constructs in vitro with dissociation equilibrium constants of 200-300 nm YaaA binds DNA with positive cooperativity, forming multiple shifted species in electrophoretic mobility shift assays. The 1.65-Å resolution X-ray crystal structure of YaaA reveals that the protein possesses a new fold that we name the cantaloupe fold. YaaA has a positively charged cleft and a helix-hairpin-helix DNA-binding motif found in other DNA repair enzymes. Our results demonstrate that YaaA is a new type of DNA-binding protein associated with the oxidative stress response and that this molecular function is likely conserved in other DUF328 family members.

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Organizational Affiliation: 

Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0246 protein YaaA	A, B	278	Escherichia coli K-12	Mutation(s): 0  Gene Names: yaaA, b0006, JW0005
Find proteins for P0A8I3 (Escherichia coli (strain K12)) Explore P0A8I3  Go to UniProtKB:  P0A8I3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	A	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.176 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.664	α = 90
b = 77.06	β = 90
c = 184.161	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-29 
• Released Date: 2016-02-24 
Deposition Author(s): Prahlad, J., Lin, J., Wilson, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM092999

Revision History 

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2020-07-08
  Changes: Data collection
• Version 1.4: 2020-10-28
  Changes: Database references