1YFJ | pdb_00001yfj

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact

• PDB DOI: https://doi.org/10.2210/pdb1YFJ/pdb
• NAKB: 1YFJ

• Classification: TRANSFERASE/DNA
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-02 Released: 2005-05-17 
• Deposition Author(s): Horton, J.R., Liebert, K., Hattman, S., Jeltsch, A., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.

Horton, J.R., Liebert, K., Hattman, S., Jeltsch, A., Cheng, X.

(2005) Cell 121: 349-361

• PubMed: 15882618 
• DOI: https://doi.org/10.1016/j.cell.2005.02.021
• Primary Citation Related Structures: 
  1YF3, 1YFJ, 1YFL


• PubMed Abstract: 
  

  DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 231.15 kDa 
• Atom Count: 15,008 
• Modeled Residue Count: 1,666 
• Deposited Residue Count: 1,704 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA adenine methylase	K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F]	259	Tequatrovirus T4	Mutation(s): 0  Gene Names: DAM EC: 2.1.1.72
UniProt
Find proteins for P04392 (Enterobacteria phage T4) Explore P04392  Go to UniProtKB:  P04392

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'	A [auth 1], B [auth 2], C [auth 3], D [auth 4], E [auth 5], F [auth 6], G [auth 7], H [auth 8], I [auth 9], J [auth 0]	15	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	AA [auth E], BA [auth F], W [auth A], X [auth B], Y [auth C], Z [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CA	T [auth 2], U [auth 4]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	Q [auth 1], R [auth 2], S [auth 2], V [auth 8]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.2	α = 90
b = 133	β = 90
c = 189.2	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
GLRF	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-17 
Deposition Author(s): Horton, J.R., Liebert, K., Hattman, S., Jeltsch, A., Cheng, X.

Revision History  

• Version 1.0: 2005-05-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Database references
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description