Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 84.24 kDa 
• Atom Count: 7,450 
• Modelled Residue Count: 740 
• Deposited Residue Count: 744 
• Unique protein chains: 1

 4ZWV

Crystal Structure of Aminotransferase AtmS13 from Actinomadura melliaura

• PDB DOI:  https://doi.org/10.2210/pdb4ZWV/pdb
• Entry: 4ZWV supersedes: 4RXK

• Classification: TRANSFERASE
• Organism(s): Actinomadura melliaura
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-19 Released: 2015-06-03 
• Deposition Author(s): Kim, Y., Bigelow, L., Endres, M., Wang, F., Phillips Jr., G.N., Joachimiak, A., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 

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 of 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: 

Department of Chemistry, Rice University, Houston, Texas, 77005.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aminotransferase	A, B	372	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
GOL	C [auth A], D [auth A], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.137	α = 90
b = 73.025	β = 103.68
c = 58.607	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing
SHELXDE	phasing
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Kim, Y., Bigelow, L., Endres, M., Wang, F., Phillips Jr., G.N., Joachimiak, A., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 4RXK

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA84374
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-06-24
  Changes: Database references
• Version 1.2: 2015-07-01
  Changes: Structure summary
• Version 1.3: 2015-07-29
  Changes: Database references
• Version 1.4: 2015-10-14
  Changes: Data collection
• Version 2.0: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2019-12-04
  Changes: Author supporting evidence