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:  
    4ZWV, 4XAU

  • 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) ...

    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
Expand
  • Reference Sequence
Small Molecules
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  (Full details and data files)

  • 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