4ZWV

Crystal Structure of Aminotransferase AtmS13 from Actinomadura melliaura


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 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative aminotransferaseA, B372Actinomadura melliauraMutation(s): 0 
Gene Names: atS13
Find proteins for Q0H2X1 (Actinomadura melliaura)
Explore Q0H2X1 
Go to UniProtKB:  Q0H2X1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A,BL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 204.137α = 90
b = 73.025β = 103.68
c = 58.607γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing
SHELXDEphasing
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA84374
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094585

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