6EF6

Structure of the microcompartment-associated aminopropanol kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and kinetic characterization of (S)-1-amino-2-propanol kinase from the aminoacetone utilization microcompartment ofMycobacterium smegmatis.

Mallette, E.Kimber, M.S.

(2018) J Biol Chem 293: 19909-19918

  • DOI: 10.1074/jbc.RA118.005485
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bacterial microcompartments encapsulate enzymatic pathways that generate small, volatile, aldehyde intermediates. The Rhodococcus and Mycobacterium microcompartment (RMM) operon from Mycobacterium smegmatis encodes four enz ...

    Bacterial microcompartments encapsulate enzymatic pathways that generate small, volatile, aldehyde intermediates. The Rhodococcus and Mycobacterium microcompartment (RMM) operon from Mycobacterium smegmatis encodes four enzymes, including ( S )-1-amino-2-propanol dehydrogenase and a likely propionaldehyde dehydrogenase. We show here that a third enzyme (and its nonmicrocompartment-associated paralog) is a moderately specific ( S )-1-amino-2-propanol kinase. We determined the structure of apo-aminopropanol kinase at 1.35 Å, revealing that it has structural similarity to hexosamine kinases, choline kinases, and aminoglycoside phosphotransferases. We modeled substrate binding, and tested our model by characterizing key enzyme variants. Bioinformatics analysis established that this enzyme is widespread in Actinobacteria, Proteobacteria, and Firmicutes, and is very commonly associated with a candidate phospholyase. In Rhizobia, aminopropanol kinase is generally associated with aromatic degradation pathways. In the RMM (and the parallel pathway that includes the second paralog), aminopropanol kinase likely degrades aminoacetone through a propanolamine-phosphate phospho-lyase-dependent pathway. These enzymatic activities were originally described in Pseudomonas , but the proteins responsible have not been previously identified. Bacterial microcompartments typically co-encapsulate enzymes which can regenerate required co-factors, but the RMM enzymes require four biochemically distinct co-factors with no overlap. This suggests that either the RMM shell can uniquely transport multiple co-factors in stoichiometric quantities, or that all enzymes except the phospho-lyase reside outside of the shell. In summary, aminopropanol kinase is a novel enzyme found in diverse bacteria and multiple metabolic pathways; its presence in the RMM implies that this microcompartment degrades aminoacetone, using a pathway that appears to violate some established precepts as to how microcompartments function.


    Organizational Affiliation

    From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada mkimber@uoguelph.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside phosphotransferase
A
354Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0270
Find proteins for A0QP47 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QP47
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download CCD File 
A
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
JFN
Query on JFN

Download CCD File 
A
(2R)-1-methoxypropan-2-amine
C4 H11 N O
NXMXETCTWNXSFG-SCSAIBSYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.01α = 90
b = 70.05β = 95.12
c = 60.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

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: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence