Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15604.01 
• Atom Count: 1004 
• Residue Count: 135 
• Unique protein chains: 1

4IAG

Crystal structure of ZbmA, the zorbamycin binding protein from Streptomyces flavoviridis

• DOI: 10.2210/pdb4IAG/pdb

• Classification: Zorbamycin Binding Protein
• Organism(s): Streptomyces flavoviridis
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2012-12-06 Released: 2013-02-20 
• Deposition Author(s): Cuff, M.E., Bigelow, L., Bruno, C.J.P., Clancy, S., Babnigg, G., Bingman, C.A., Yennamalli, R., Lohman, J., Ma, M., Shen, B., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.231 
• R-Value Work: 0.189 

Literature

Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.

Rudolf, J.D., Bigelow, L., Chang, C., Cuff, M.E., Lohman, J.R., Chang, C.Y., Ma, M., Yang, D., Clancy, S., Babnigg, G., Joachimiak, A., Phillips, G.N., Shen, B.

(2015) Biochemistry 54: 6842-6851

• PubMed: 26512730 
• DOI: 10.1021/acs.biochem.5b01008
• Primary Citation of Related Structures:  
  5CJ3


• PubMed Abstract: 
  

The bleomycins (BLMs), tallysomycins (TLMs), phleomycin, and zorbamycin (ZBM) are members of the BLM family of glycopeptide-derived antitumor antibiotics. The BLM-producing Streptomyces verticillus ATCC15003 and the TLM-producing Streptoalloteichus hindustanus E465-94 ATCC31158 both possess at least two self-resistance elements, an N-acetyltransferase and a binding protein. The N-acetyltransferase provides resistance by disrupting the metal-binding domain of the antibiotic that is required for activity, while the binding protein confers resistance by sequestering the metal-bound antibiotic and preventing drug activation via molecular oxygen. We recently established that the ZBM producer, Streptomyces flavoviridis ATCC21892, lacks the N-acetyltransferase resistance gene and that the ZBM-binding protein, ZbmA, is sufficient to confer resistance in the producing strain. To investigate the resistance mechanism attributed to ZbmA, we determined the crystal structures of apo and Cu(II)-ZBM-bound ZbmA at high resolutions of 1.90 and 1.65 Å, respectively. A comparison and contrast with other structurally characterized members of the BLM-binding protein family revealed key differences in the protein-ligand binding environment that fine-tunes the ability of ZbmA to sequester metal-bound ZBM and supports drug sequestration as the primary resistance mechanism in the producing organisms of the BLM family of antitumor antibiotics.

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Organizational Affiliation: 

Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Zbm binding protein	A	135	Streptomyces flavoviridis	Mutation(s): 0  Gene Names: zbmA
Find proteins for B9UIZ4 (Streptomyces flavoviridis) Go to UniProtKB:  B9UIZ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ILY	A	NON-POLYMER	C9 H20 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.231 
• R-Value Work: 0.189 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 38.787	α = 90.00
b = 38.787	β = 90.00
c = 268.524	γ = 120.00

Software Package:

Software Name	Purpose
SOLVE	phasing
DENZO	data reduction
Coot	model building
HKL-3000	data scaling
SBC-Collect	data collection
HKL-3000	phasing
PDB_EXTRACT	data extraction
CCP4	phasing
SCALEPACK	data scaling
SHELXE	model building
DM	phasing
RESOLVE	phasing
REFMAC	refinement
ARP/wARP	model building
MLPHARE	phasing
O	model building
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-06 
• Released Date: 2013-02-20 
• Deposition Author(s): Cuff, M.E., Bigelow, L., Bruno, C.J.P., Clancy, S., Babnigg, G., Bingman, C.A., Yennamalli, R., Lohman, J., Ma, M., Shen, B., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History 

• Version 1.0: 2013-02-20
  Type: Initial release
• Version 1.1: 2013-12-25
  Type: Structure summary
• Version 1.2: 2015-11-11
  Type: Database references
• Version 1.3: 2015-12-02
  Type: Database references
• Version 1.4: 2017-11-15
  Type: Refinement description