5LOG | pdb_00005log

Crystal Structure of SafC from Myxococcus xanthus bound to SAM

• PDB DOI: https://doi.org/10.2210/pdb5LOG/pdb

• Classification: TRANSFERASE
• Organism(s): Myxococcus xanthus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-08-09 Released: 2017-06-21 
• Deposition Author(s): Gerhardt, S., Netzer, J., Einsle, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.212 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Functional and structural characterisation of a bacterial O-methyltransferase and factors determining regioselectivity.

Siegrist, J., Netzer, J., Mordhorst, S., Karst, L., Gerhardt, S., Einsle, O., Richter, M., Andexer, J.N.

(2017) FEBS Lett 591: 312-321

• PubMed: 27990630 
• DOI: https://doi.org/10.1002/1873-3468.12530
• Primary Citation Related Structures: 
  5LHM, 5LOG


• PubMed Abstract: 
  

  Mg ²⁺ -dependent catechol-O-methyltransferases occur in animals as well as in bacteria, fungi and plants, often with a pronounced selectivity towards one of the substrate's hydroxyl groups. Here, we show that the bacterial MxSafC exhibits excellent regioselectivity for para as well as for meta methylation, depending on the substrate's characteristics. The crystal structure of MxSafC was solved in apo and in holo form. The structure complexed with a full set of substrates clearly illustrates the plasticity of the active site region. The awareness that a wide range of factors influences the regioselectivity will aid the further development of catechol-O-methyltransferases as well as other methyltransferases as selective and efficient biocatalysts for chemical synthesis.

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Organizational Affiliation: 
• Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Germany.
Institute of Biochemistry, Albert-Ludwigs-University Freiburg, Germany.
BIOSS Centre for Biological Signalling Studies, Freiburg, Germany.
Bio-, Electro- and Chemocatalysis BioCat, Straubing Branch, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Straubing, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.15 kDa 
• Atom Count: 3,806 
• Modeled Residue Count: 440 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative O-methyltransferase	A, B	233	Myxococcus xanthus	Mutation(s): 1  Gene Names: safC
UniProt
Find proteins for Q50859 (Myxococcus xanthus) Explore Q50859  Go to UniProtKB:  Q50859

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
LDP	F [auth A]	L-DOPAMINE C8 H11 N O2 VYFYYTLLBUKUHU-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.212 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.84	α = 90
b = 51.017	β = 98.58
c = 72.677	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Gerhardt, S., Netzer, J., Einsle, O.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2025-12-10
  Changes: Data collection, Structure summary