6CI8

Structure of the microcompartment-associated aminoacetone dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis.

Mallette, E.Kimber, M.S.

(2018) Biochemistry 57: 3780-3789

  • DOI: 10.1021/acs.biochem.8b00464
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • S-(+)-1-Amino-2-propanol dehydrogenase (APDH) is a short-chain dehydrogenase/reductase associated with the incompletely characterized Rhodococcus and Mycobacterium bacterial microcompartment (RMM). We enzymatically characterized the APDH from M. smeg ...

    S-(+)-1-Amino-2-propanol dehydrogenase (APDH) is a short-chain dehydrogenase/reductase associated with the incompletely characterized Rhodococcus and Mycobacterium bacterial microcompartment (RMM). We enzymatically characterized the APDH from M. smegmatis and showed it is highly selective, with a low micromolar K m for S-(+)-1-amino-2-propanol and specificity for NADP(H). A paralogous enzyme from a nonmicrocompartment-associated operon in the same organism was also shown to have a similar activity. We determined the structure of APDH in both apo form (at 1.7 Å) and as a ternary enzyme complex with NADP + and aminoacetone (at 1.9 Å). Recognition of aminoacetone was mediated by strong hydrogen bonds to the amino group by Thr145 and by Glu251 from the C-terminus of an adjacent protomer. The substrate binding site entirely encloses the substrate, with close contacts between the aminoacetone methyl group and Phe95, Trp154, and Leu195. Kinetic characterization of several of these residues confirm their importance in enzyme functioning. Bioinformatics analysis of APDH homologues implies that many nonmicrocompartment APDH orthologues partake in an aminoacetone degradation pathway that proceeds via an aminopropanol O-phosphate phospholyase. RMM microcompartments may mediate a similar pathway, though possibly with differences in the details of the pathway that necessitates encapsulation behind a shell.


    Organizational Affiliation

    Department of Molecular and Cellular Biology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-oxoacyl-[acyl-carrier-protein] reductase
A, B
262Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0269
EC: 1.1.1.100
Find proteins for A0QP46 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QP46
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.24α = 90
b = 104.24β = 90
c = 80.86γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada04045-2015

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence