1NMN | pdb_00001nmn

Structure of yqgF from Escherichia coli, a hypothetical protein

• PDB DOI: https://doi.org/10.2210/pdb1NMN/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-10 Released: 2004-03-02 
• Deposition Author(s): Galkin, A., Sarikaya, E., Krajewski, W., Howard, A., Herzberg, O., Structure 2 Function Project (S2F)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 

Literature

The Crystal Structure and Biochemical Analyses of Escherichia coli YqgF Illuminate Its Diverse Functions.

Thakur, M., Dhyani, K.M., Galkin, A., Krajewski, W.W., Yavasani, S., Demirkan, E., Howard, A., Herzberg, O., Muniyappa, K.

(2025) J Mol Biology 437: 169221-169221

• PubMed: 40398672 
• DOI: https://doi.org/10.1016/j.jmb.2025.169221
• Primary Citation of Related Structures:  
  1NMN, 1NU0


• PubMed Abstract: 
  

  The Escherichia coli yqgF gene product is essential for bacterial growth and to confer resistance to multiple antimicrobial agents. Furthermore, additional evidence suggests that YqgF, a RuvC family protein, is required for DNA damage repair, yet the mechanism underlying its action remains elusive. To address this knowledge gap, we conducted structural and biochemical investigations on E. coli YqgF (EcYqgF). Here, we reveal that EcYqgF binds preferentially to branched DNA structures compared to single-stranded (ssDNA) and double-stranded DNA (dsDNA), and that the EcYqgF:DNA complexes formed with branched DNA species were more stable and resistant against high salt and excess of competitor DNA than those formed with dsDNA. We show that EcYqgF has a strong preference towards cleavage of branched DNA structures than dsDNA, ssDNA, and dsDNA with 5'- or 3'-ssDNA overhangs. Crucially, we found that EcYqgF has a DNA-independent, Mg ²⁺ -dependent ATPase activity that is tightly coupled to DNA cleavage. We have determined the crystal structure of EcYqgF, developed a model of ATP binding using AI-based methods, and rationalized the impact of site-directed mutants on ATP binding. Furthermore, we discovered two unusual ATPase-defective EcYqgF variants, proficient in ATP-binding but not hydrolysis, which display a modest increase in the DNA-binding affinity, yet are devoid of endonucleolytic activity, thus revealing a previously unappreciated property of YqgF endonucleases. Collectively, our results suggest that despite its overall structural similarity to the well-studied resolvase, RuvC, EcYqgF is functionally distinct. Importantly, the EcYqgF dual activity that couples ATP hydrolysis to endonuclease activity is absent in RuvC.

---

Organizational Affiliation: 
• Sri Venkateswara College, University of Delhi, New Delhi 110021, India. Electronic address: [e-mail].
Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA; Institute of Bioscience and Biotechnology, University of Maryland, Rockville, MD 20850, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA; Biology Department, Faculty of Arts and Sciences, Bursa Uludag University, Turkey.
Biology Department, Illinois Institute of Technology, Chicago, IL 60616, USA.
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA; Institute of Bioscience and Biotechnology, University of Maryland, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland College Park, MD 20742, USA. Electronic address: [e-mail].
Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.41 kDa 
• Atom Count: 2,005 
• Modeled Residue Count: 237 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yqgF	A, B	138	Escherichia coli	Mutation(s): 0  Gene Names: YQGF EC: 3.1
UniProt
Find proteins for P0A8I1 (Escherichia coli (strain K12)) Explore P0A8I1  Go to UniProtKB:  P0A8I1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.5	α = 90
b = 61.7	β = 90
c = 68.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-02 
Deposition Author(s): Galkin, A., Sarikaya, E., Krajewski, W., Howard, A., Herzberg, O., Structure 2 Function Project (S2F)

Revision History  

• Version 1.0: 2004-03-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references
• Version 1.4: 2025-06-18
  Changes: Database references, Structure summary