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 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1038/nchembio.556
  • Primary Citation of Related Structures:  
    2WDW, 5AWV

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative hexose oxidase
A, B, C, D
523Nonomuraea gerenzanensisMutation(s): 0 
Gene Names: dbv29
UniProt
Find proteins for Q7WZ62 (Nonomuraea gerenzanensis)
Explore Q7WZ62 
Go to UniProtKB:  Q7WZ62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WZ62
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TEICOPLANIN7Actinoplanes teichomyceticusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
M [auth A],
O [auth B],
R [auth C],
T [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth K]
EA [auth L]
IA [auth M]
MA [auth N]
QA [auth O]
BA [auth K],
EA [auth L],
IA [auth M],
MA [auth N],
QA [auth O],
VA [auth P],
W [auth I],
Y [auth J]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
N1L
Query on N1L

Download Ideal Coordinates CCD File 
CA [auth K]
FA [auth L]
JA [auth M]
NA [auth N]
RA [auth O]
CA [auth K],
FA [auth L],
JA [auth M],
NA [auth N],
RA [auth O],
WA [auth P]
2-amino-2-deoxy-beta-D-glucopyranuronic acid
C6 H11 N O6
CRIPFXSBMSGPKB-LVBGKUAWSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
N [auth A],
Q [auth B],
S [auth C],
SA [auth O],
U [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
AA [auth K]
DA [auth L]
HA [auth M]
LA [auth N]
PA [auth O]
AA [auth K],
DA [auth L],
HA [auth M],
LA [auth N],
PA [auth O],
UA [auth P],
V [auth I],
X [auth J]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
T55
Query on T55

Download Ideal Coordinates CCD File 
GA [auth M]
KA [auth N]
OA [auth O]
P [auth B]
TA [auth P]
GA [auth M],
KA [auth N],
OA [auth O],
P [auth B],
TA [auth P],
Z [auth K]
8-METHYLNONANOIC ACID
C10 H20 O2
OAOABCKPVCUNKO-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
3MY
Query on 3MY
E [auth I]
F [auth J]
G [auth K]
H [auth L]
I [auth M]
E [auth I],
F [auth J],
G [auth K],
H [auth L],
I [auth M],
J [auth N],
K [auth O],
L [auth P]
D-PEPTIDE LINKINGC9 H10 Cl N O3TYR
OMY
Query on OMY
E [auth I]
F [auth J]
G [auth K]
H [auth L]
I [auth M]
E [auth I],
F [auth J],
G [auth K],
H [auth L],
I [auth M],
J [auth N],
K [auth O],
L [auth P]
L-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_001065
Query on PRD_001065
E [auth I]
F [auth J]
G [auth K]
H [auth L]
I [auth M]
E [auth I],
F [auth J],
G [auth K],
H [auth L],
I [auth M],
J [auth N],
K [auth O],
L [auth P]
teicoplaninGlycopeptide / Antibiotic, Antimicrobial
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.791α = 90
b = 150.778β = 98.4
c = 124.853γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2023-11-15
    Changes: Data collection, Derived calculations