Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 64991.08 
• Atom Count: 4447 
• Residue Count: 561 
• Unique protein chains: 1

2CFM

ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS

• DOI: 10.2210/pdb2CFM/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
• Expression System: Escherichia coli BL21


• Deposited: 2006-02-22 Released: 2006-07-12 
• Deposition Author(s): Nishida, H., Ishino, Y., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.231 
• R-Value Work: 0.204 

Literature

The Closed Structure of an Archaeal DNA Ligase from Pyrococcus Furiosus.

Nishida, H., Kiyonari, S., Ishino, Y., Morikawa, K.

(2006) J.Mol.Biol. 360: 956

• PubMed: 16820169 
• DOI: 10.1016/j.jmb.2006.05.062


• PubMed Abstract: 
  

DNA ligases join single-strand breaks in double-stranded DNA, and are essential to maintain genome integrity in DNA metabolism. Here, we report the 1.8 A resolution structure of Pyrococcus furiosus DNA ligase (PfuLig), which represents the first full-length atomic view of an ATP-dependent eukaryotic-type DNA ligase. The enzyme comprises the N-terminal DNA-binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The architecture of each domain resembles those of human DNA ligase I, but the domain arrangements differ strikingly between the two enzymes. The closed conformation of the two "catalytic core" domains at the carboxyl terminus in PfuLig creates a small compartment, which holds a non-covalently bound AMP molecule. This domain rearrangement results from the "domain-connecting" role of the helical extension conserved at the C termini in archaeal and eukaryotic DNA ligases. The DNA substrate in the human open-ligase is replaced by motif VI in the Pfu closed-ligase. Both the shapes and electrostatic distributions are similar between motif VI and the DNA substrate, suggesting that motif VI in the closed state mimics the incoming substrate DNA. Two basic residues (R531 and K534) in motif VI reside within the active site pocket and interact with the phosphate group of the bound AMP. The crystallographic and functional analyses of mutant enzymes revealed that these two residues within the RxDK sequence play essential and complementary roles in ATP processing. This sequence is also conserved exclusively among the covalent nucleotidyltransferases, even including mRNA-capping enzymes with similar helical extensions at the C termini.

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Organizational Affiliation: 

Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), Osaka 565-0874, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
THERMOSTABLE DNA LIGASE	A	561	Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)	Mutation(s): 0  Gene Names: lig EC: 6.5.1.1
Find proteins for P56709 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Go to UniProtKB:  P56709

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
AMP	A	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-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: 1.8 Å
• R-Value Free: 0.231 
• R-Value Work: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.866	α = 90.00
b = 87.399	β = 109.22
c = 62.648	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-22 
• Released Date: 2006-07-12 
• Deposition Author(s): Nishida, H., Ishino, Y., Morikawa, K.

Revision History 

• Version 1.0: 2006-07-12
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-01-30
  Type: Data collection, Experimental preparation, Other
• Version 1.4: 2019-02-06
  Type: Data collection, Experimental preparation