4XCA

Crystal Structure of HygX from Streptomyces hygroscopicus with nickel and 2-oxoglutarate bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.

McCulloch, K.M.McCranie, E.K.Smith, J.A.Sarwar, M.Mathieu, J.L.Gitschlag, B.L.Du, Y.Bachmann, B.O.Iverson, T.M.

(2015) Proc Natl Acad Sci U S A 112: 11547-11552

  • DOI: 10.1073/pnas.1500964112
  • Primary Citation of Related Structures:  
    4XAA, 4XAB, 4XAC, 4XBZ, 4XC9, 4XCA, 4XCB, 4ZPI

  • PubMed Abstract: 
  • Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge ...

    Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. We have identified a conserved group of nonheme iron, α-ketoglutarate-dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases of everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.


    Organizational Affiliation

    Department of Pharmacology, Vanderbilt University, Nashville, TN 37232; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232 brian.bachmann@vanderbilt.edu tina.iverson@vanderbilt.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
oxidase/hydroxylaseA, B, C, D258Streptomyces hygroscopicus subsp. hygroscopicusMutation(s): 0 
Gene Names: hygX
UniProt
Find proteins for Q2MFS1 (Streptomyces hygroscopicus subsp. hygroscopicus)
Explore Q2MFS1 
Go to UniProtKB:  Q2MFS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2MFS1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
CS
Query on CS

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C],
P [auth D]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.399α = 90
b = 112.044β = 90
c = 177.803γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesT32 HL007751
American Heart AssociationUnited States12GRNT11920011

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2015-09-30
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence