5AWV

Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds.

Liu, Y.C.Li, Y.S.Lyu, S.Y.Hsu, L.J.Chen, Y.H.Huang, Y.T.Chan, H.C.Huang, C.J.Chen, G.H.Chou, C.C.Tsai, M.D.Li, T.L.

(2011) Nat. Chem. Biol. 7: 304-309

  • DOI: 10.1038/nchembio.556
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the search for new efficacious antibiotics, biosynthetic engineering offers attractive opportunities to introduce minor alterations to antibiotic structures that may overcome resistance. Dbv29, a flavin-containing oxidase, catalyzes the four-elect ...

    In the search for new efficacious antibiotics, biosynthetic engineering offers attractive opportunities to introduce minor alterations to antibiotic structures that may overcome resistance. Dbv29, a flavin-containing oxidase, catalyzes the four-electron oxidation of a vancomycin-like glycopeptide to yield A40926. Structural and biochemical examination of Dbv29 now provides insights into residues that govern flavinylation and activity, protein conformation and reaction mechanism. In particular, the serendipitous discovery of a reaction intermediate in the crystal structure led us to identify an unexpected opportunity to intercept the normal enzyme mechanism at two different points to create new teicoplanin analogs. Using this method, we synthesized families of antibiotic analogs with amidated and aminated lipid chains, some of which showed marked potency and efficacy against multidrug resistant pathogens. This method offers a new strategy for the development of chemical diversity to combat antibacterial resistance.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative hexose oxidase
A, B, C, D
523Nonomuraea gerenzanensisMutation(s): 0 
Gene Names: dbv29
Find proteins for Q7WZ62 (Nonomuraea gerenzanensis)
Go to UniProtKB:  Q7WZ62
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TEICOPLANIN
I, J, K, L, M, N, O, P
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B, C, D, O
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
I, J, K, L, M, N, O, P
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
I, J, K, L, M, N, O, P
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
N1L
Query on N1L

Download SDF File 
Download CCD File 
K, L, M, N, O, P
2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANURONIC ACID
C6 H11 N O6
CRIPFXSBMSGPKB-LVBGKUAWSA-N
 Ligand Interaction
T55
Query on T55

Download SDF File 
Download CCD File 
B, K, M, N, O, P
8-METHYLNONANOIC ACID
C10 H20 O2
OAOABCKPVCUNKO-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 2 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001065
Query on PRD_001065
B,I,J,K,L,M,N,O,PteicoplaninGlycopeptide / Antibiotic, Antimicrobial

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PRD_001065
Query on PRD_001065
I,J,K,L,M,N,O,PteicoplaninGlycopeptide / Antibiotic, Antimicrobial

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.791α = 90.00
b = 150.778β = 98.40
c = 124.853γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-09 
  • Released Date: 2015-08-19 
  • Deposition Author(s): Liu, Y.C., Li, T.L.
  • This entry supersedes: 4K3T

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwan96-2628-B-001-026-MY3
Ministry of Science and TechnologyTaiwan98-2311-B-001-014-MY3

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release