1Q0T | pdb_00001q0t

Ternary Structure of T4DAM with AdoHcy and DNA

• PDB DOI: https://doi.org/10.2210/pdb1Q0T/pdb
• NAKB: 1Q0T

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


• Deposited: 2003-07-17 Released: 2003-09-23 
• Deposition Author(s): Yang, Z., Horton, J.R., Zhou, L., Zhang, X.J., Dong, A., Zhang, X., Schlagman, S.L., Kossykh, V., Hattman, S., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.293 (Depositor) 
• R-Value Work: 
  0.238 (Depositor) 

Literature

Structure of the bacteriophage T4 DNA adenine methyltransferase

Yang, Z., Horton, J.R., Zhou, L., Zhang, X.J., Dong, A., Zhang, X., Schlagman, S.L., Kossykh, V., Hattman, S., Cheng, X.

(2003) Nat Struct Biol 10: 849-855

• PubMed: 12937411 
• DOI: https://doi.org/10.1038/nsb973
• Primary Citation Related Structures: 
  1Q0S, 1Q0T


• PubMed Abstract: 
  

  DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a beta-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.28 kDa 
• Atom Count: 4,538 
• Modeled Residue Count: 506 
• Deposited Residue Count: 542 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA adenine methylase	C [auth A], D [auth B]	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(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'	A [auth C], B [auth D]	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	G [auth A], H [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
IOD	E [auth C], F [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.293 (Depositor) 
• R-Value Work:  0.238 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.7	α = 90
b = 109.7	β = 104.2
c = 73.6	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-23 
Deposition Author(s): Yang, Z., Horton, J.R., Zhou, L., Zhang, X.J., Dong, A., Zhang, X., Schlagman, S.L., Kossykh, V., Hattman, S., Cheng, X.

Revision History  

• Version 1.0: 2003-09-23
  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: 2020-07-22
  Changes: Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations