4O1F | pdb_00004o1f

Structure of a methyltransferase component in complex with THF involved in O-demethylation

• PDB DOI: https://doi.org/10.2210/pdb4O1F/pdb

• Classification: TRANSFERASE
• Organism(s): Desulfitobacterium hafniense DCB-2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-15 Released: 2015-01-21 
• Deposition Author(s): Sjuts, H., Dunstan, M.S., Fisher, K., Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.245 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-demethylase shed light on methyltetrahydrofolate formation

Sjuts, H., Dunstan, M.S., Fisher, K., Leys, D.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1900-1908

• PubMed: 26327380 
• DOI: https://doi.org/10.1107/S1399004715013061
• Primary Citation Related Structures: 
  4O0Q, 4O1E, 4O1F


• PubMed Abstract: 
  

  O-Demethylation by acetogenic or organohalide-respiring bacteria leads to the formation of methyltetrahydrofolate from aromatic methyl ethers. O-Demethylases, which are cobalamin-dependent, three-component enzyme systems, catalyse methyl-group transfers from aromatic methyl ethers to tetrahydrofolate via methylcobalamin intermediates. In this study, crystal structures of the tetrahydrofolate-binding methyltransferase module from a Desulfitobacterium hafniense DCB-2 O-demethylase were determined both in complex with tetrahydrofolate and the product methyltetrahydrofolate. While these structures are similar to previously determined methyltransferase structures, the position of key active-site residues is subtly altered. A strictly conserved Asn is displaced to establish a putative proton-transfer network between the substrate N5 and solvent. It is proposed that this supports the efficient catalysis of methyltetrahydrofolate formation, which is necessary for efficient O-demethylation.

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Organizational Affiliation: 
• Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 64.4 kDa 
• Atom Count: 4,399 
• Modeled Residue Count: 535 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate synthase DHPS	A, B	290	Desulfitobacterium hafniense DCB-2	Mutation(s): 0  Gene Names: Dhaf_0722
UniProt
Find proteins for B8FW00 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FW00  Go to UniProtKB:  B8FW00

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THG	C [auth A], D [auth B]	(6S)-5,6,7,8-TETRAHYDROFOLATE C19 H23 N7 O6 MSTNYGQPCMXVAQ-RYUDHWBXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.245 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.19	α = 90
b = 118.24	β = 90
c = 57.71	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Sjuts, H., Dunstan, M.S., Fisher, K., Leys, D.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2015-09-16
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description