4XO0

Crystal structure of 5'-CTTATPPTAZZATAAG in a host-guest complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for a six nucleotide genetic alphabet.

Georgiadis, M.M.Singh, I.Kellett, W.F.Hoshika, S.Benner, S.A.Richards, N.G.

(2015) J. Am. Chem. Soc. 137: 6947-6955

  • DOI: 10.1021/jacs.5b03482
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be ...

    Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.



Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
reverse transcriptase
A
259Moloney murine leukemia virusMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus)
Go to UniProtKB:  P03355
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*T)-3')B8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')G8synthetic construct
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
1W5
Query on 1W5
G
DNA linkingC10 H14 N3 O9 P

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1WA
Query on 1WA
B
DNA LINKINGC10 H16 N5 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.638α = 90.00
b = 145.359β = 90.00
c = 46.878γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM111386

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Non-polymer description
  • Version 1.2: 2017-01-11
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Refinement description