Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 28.72 kDa 
• Atom Count: 2274 
• Modelled Residue Count: 238 
• Deposited Residue Count: 254 
• Unique protein chains: 1

5T38

Crystal Structure of the N-terminal domain of EvdMO1 with SAH bound

• PDB DOI: 10.2210/pdb5T38/pdb

• Classification: TRANSFERASE
• Organism(s): Micromonospora carbonacea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-25 Released: 2017-09-06 
• Deposition Author(s): McCulloch, K.M., Berndt, S., Yamakawa, I., Chen, Q., Loukachevitch, L.V., Starbird, C., Perry, N.A., Iverson, T.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Heart Association, National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.168 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Literature

The Structure of the Bifunctional Everninomicin Biosynthetic Enzyme EvdMO1 Suggests Independent Activity of the Fused Methyltransferase-Oxidase Domains.

Starbird, C.A., Perry, N.A., Chen, Q., Berndt, S., Yamakawa, I., Loukachevitch, L.V., Limbrick, E.M., Bachmann, B.O., Iverson, T.M., McCulloch, K.M.

(2018) Biochemistry 57: 6827-6837

• PubMed: 30525509 
• DOI: 10.1021/acs.biochem.8b00836
• Primary Citation of Related Structures:  
  5T38, 5T39, 6EC3


• PubMed Abstract: 
  

Members of the orthosomycin family of natural products are decorated polysaccharides with potent antibiotic activity and complex biosynthetic pathways. The defining feature of the orthosomycins is an orthoester linkage between carbohydrate moieties that is necessary for antibiotic activity and is likely formed by a family of conserved oxygenases. Everninomicins are octasaccharide orthosomycins produced by Micromonospora carbonacea that have two orthoester linkages and a methylenedioxy bridge, three features whose formation logically requires oxidative chemistry. Correspondingly, the evd gene cluster encoding everninomicin D encodes two monofunctional nonheme iron, α-ketoglutarate-dependent oxygenases and one bifunctional enzyme with an N-terminal methyltransferase domain and a C-terminal oxygenase domain. To investigate whether the activities of these domains are linked in the bifunctional enzyme EvdMO1, we determined the structure of the N-terminal methyltransferase domain to 1.1 Å and that of the full-length protein to 3.35 Å resolution. Both domains of EvdMO1 adopt the canonical folds of their respective superfamilies and are connected by a short linker. Each domain's active site is oriented such that it faces away from the other domain, and there is no evidence of a channel connecting the two. Our results support EvdMO1 working as a bifunctional enzyme with independent catalytic activities.

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Organizational Affiliation: 

Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, Kentucky, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EvdMO1	A	254	Micromonospora carbonacea	Mutation(s): 0  Gene Names: evdMO1, GA0070563_112238
UniProt
Find proteins for A0A1C5AE13 (Micromonospora carbonacea) Explore A0A1C5AE13  Go to UniProtKB:  A0A1C5AE13

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.168 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.15785/SBGRID/355 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.427	α = 90
b = 41.272	β = 99.8
c = 56.465	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-08-25 
• Released Date: 2017-09-06 
Deposition Author(s): McCulloch, K.M., Berndt, S., Yamakawa, I., Chen, Q., Loukachevitch, L.V., Starbird, C., Perry, N.A., Iverson, T.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01AI106987
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	T32 HL007751
American Heart Association	United States	12GRNT11920011
American Heart Association	United States	14GRNT20390021
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10 RR026915

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence