Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 45.66 kDa 
• Atom Count: 3,485 
• Modelled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 2C7P

HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (GCGC:GMPC) and SAH

• PDB DOI:  https://doi.org/10.2210/pdb2C7P/pdb
• NDB: PD0934

• Classification: TRANSFERASE/DNA
• Organism(s): Haemophilus haemolyticus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-11-25 Released: 2005-12-14 
• Deposition Author(s): Neely, R.K., Daujotyte, D., Grazulis, S., Magennis, S.W., Dryden, D.T.F., Klimasauskas, S., Jones, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.220 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes.

Neely, R.K., Daujotyte, D., Grazulis, S., Magennis, S.W., Dryden, D.T.F., Klimasauskas, S., Jones, A.C.

(2005) Nucleic Acids Res 33: 6953

• PubMed: 16340006 
• DOI: https://doi.org/10.1093/nar/gki995
• Primary Citation of Related Structures:  
  2C7O, 2C7P, 2C7Q, 2C7R


• PubMed Abstract: 
  

DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 A resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (approximately 100 ps) decay component and the large increase in the amplitude of the long (approximately 10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures.

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Organizational Affiliation: 

School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MODIFICATION METHYLASE HHAI	A	327	Haemophilus haemolyticus	Mutation(s): 0  EC: 2.1.1.37
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus) Explore P05102  Go to UniProtKB:  P05102

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3'	B [auth C]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3'	C [auth D]	12	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
EPE	J [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CIT	K [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.220 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.845	α = 90
b = 94.845	β = 90
c = 313.03	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-14 
Deposition Author(s): Neely, R.K., Daujotyte, D., Grazulis, S., Magennis, S.W., Dryden, D.T.F., Klimasauskas, S., Jones, A.C.

Revision History  

• Version 1.0: 2005-12-14
  Type: Initial release
  
• Version 1.1: 2014-01-29
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations