4XAU | pdb_00004xau

Crystal structure of AtS13 from Actinomadura melliaura

• PDB DOI: https://doi.org/10.2210/pdb4XAU/pdb

• Classification: TRANSFERASE
• Organism(s): Actinomadura melliaura
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2014-12-15 Released: 2014-12-24 
• Deposition Author(s): Wang, F., Singh, S., Xu, W., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis.

Singh, S., Kim, Y., Wang, F., Bigelow, L., Endres, M., Kharel, M.K., Babnigg, G., Bingman, C.A., Joachimiak, A., Thorson, J.S., Phillips, G.N.

(2015) Proteins 83: 1547-1554

• PubMed: 26061967 
• DOI: https://doi.org/10.1002/prot.24844
• Primary Citation Related Structures: 
  4XAU, 4ZWV


• PubMed Abstract: 
  

  AT2433 from Actinomadura melliaura is an indolocarbazole antitumor antibiotic structurally distinguished by its unique aminodideoxypentose-containing disaccharide moiety. The corresponding sugar nucleotide-based biosynthetic pathway for this unusual sugar derives from comparative genomics where AtmS13 has been suggested as the contributing sugar aminotransferase (SAT). Determination of the AtmS13 X-ray structure at 1.50-Å resolution reveals it as a member of the aspartate aminotransferase fold type I (AAT-I). Structural comparisons of AtmS13 with homologous SATs that act upon similar substrates implicate potential active site residues that contribute to distinctions in sugar C5 (hexose vs. pentose) and/or sugar C2 (deoxy vs. hydroxyl) substrate specificity.

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Organizational Affiliation: 
• Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences Division, University of Kentucky College of Pharmacy, Lexington, Kentucky, 40536-0596.
Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439.
Department of BioSciences, Rice University, Houston, Texas, 77005.
School of Pharmacy, Department of Pharmaceutical Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland.
Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706.
Department of Chemistry, Rice University, Houston, Texas, 77005.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 302.86 kDa 
• Atom Count: 20,714 
• Modeled Residue Count: 2,621 
• Deposited Residue Count: 2,723 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aminotransferase	A, B, C, D, E, F, G	389	Actinomadura melliaura	Mutation(s): 0  Gene Names: atS13
UniProt
Find proteins for Q0H2X1 (Actinomadura melliaura) Explore Q0H2X1  Go to UniProtKB:  Q0H2X1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	H [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34xau

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233.149	α = 90
b = 233.149	β = 90
c = 460.859	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Wang, F., Singh, S., Xu, W., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2015-06-24
  Changes: Database references
• Version 1.2: 2015-07-29
  Changes: Database references
• Version 1.3: 2015-08-26
  Changes: Data collection
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description