9FZX | pdb_00009fzx

Rhizobium phage ligase

• PDB DOI: https://doi.org/10.2210/pdb9FZX/pdb
• NAKB: 9FZX

• Classification: LIGASE
• Organism(s): Rhizobium phage 16-3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-06 Released: 2025-06-11 
• Deposition Author(s): Rothweiler, U., Williamson, A.
• Funding Organization(s): Research Council of Norway

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of ATP-dependent DNA ligase from Rhizobium phage vB_RleM_P10VF.

Rothweiler, U., Leiros, H.K.S., Williamson, A.

(2025) Acta Crystallogr F Struct Biol Commun 81: 249-254

• PubMed: 40365832 
• DOI: https://doi.org/10.1107/S2053230X2500411X
• Primary Citation of Related Structures:  
  9FZX


• PubMed Abstract: 
  

  DNA ligases are foundational molecular-biological tools used for cloning and sequencing workflows, and are essential replicative enzymes for all cellular life forms as well as many viruses and bacteriophage. There is considerable interest in structurally and functionally characterizing novel DNA ligases and profiling their suitability for molecular-biological applications. Here, we report the crystal structure of the ATP-dependent DNA ligase from the Rhizobium phage vB_RleM_P10VF bound to a nicked DNA duplex determined to 2.2 Å resolution. The enzyme crystallized in the DNA-encircling conformation, arrested as a step 2 intermediate in the catalytic cycle with the adenylating cofactor transferred to the 5'-phosphate of the DNA nick. The overall structure of the DNA ligase closely resembles that of the T4 DNA ligase, including an α-helical globular DNA-binding domain. Several secondary-structural elements are abbreviated in the P10VF DNA ligase relative to the T4 DNA ligase enzyme, which may account for its lower specific activity, especially on DNA substrates containing double-stranded breaks.

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Organizational Affiliation: 
• ArcticZymes Technologies ASA, 9037 Tromsø, Norway.
The Norwegian Structural Biology Centre, UiT The Arctic University of Norway, Forskningsparken 3, 9037 Tromsø, Norway.
School of Science, University of Waikato, Hamilton 3216, New Zealand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.52 kDa 
• Atom Count: 4,191 
• Modeled Residue Count: 428 
• Deposited Residue Count: 462 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	420	Rhizobium phage 16-3	Mutation(s): 0  Gene Names: P10VF_217
UniProt
Find proteins for A0A076YM08 (Rhizobium phage vB_RleM_P10VF) Explore A0A076YM08  Go to UniProtKB:  A0A076YM08

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')	B	21	Rhizobium phage 16-3

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	C	10	Rhizobium phage 16-3

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')	D	11	Rhizobium phage 16-3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	F [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
BTB	E [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.039	α = 90
b = 100.392	β = 90
c = 107.692	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Rothweiler, U., Williamson, A.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release