5JFM

Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound propionyl-CoA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Literature

In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment.

Zarzycki, J., Sutter, M., Cortina, N.S., Erb, T.J., Kerfeld, C.A.

(2017) Sci Rep 7: 42757-42757

  • DOI: 10.1038/srep42757
  • Primary Citation of Related Structures:  
    5JFL, 5JFM, 5JFN

  • PubMed Abstract: 

    • Many bacteria encode proteinaceous bacterial microcompartments (BMCs) that encapsulate sequential enzymatic reactions of diverse metabolic pathways. Well-characterized BMCs include carboxysomes for CO 2 -fixation, and propanediol- and ethanolamine-utilizing microcompartments that contain B 12 -dependent enzymes ...

    Many bacteria encode proteinaceous bacterial microcompartments (BMCs) that encapsulate sequential enzymatic reactions of diverse metabolic pathways. Well-characterized BMCs include carboxysomes for CO 2 -fixation, and propanediol- and ethanolamine-utilizing microcompartments that contain B 12 -dependent enzymes. Genes required to form BMCs are typically organized in gene clusters, which promoted their distribution across phyla by horizontal gene transfer. Recently, BMCs associated with glycyl radical enzymes (GREs) were discovered; these are widespread and comprise at least three functionally distinct types. Previously, we predicted one type of these GRE-associated microcompartments (GRMs) represents a B 12 -independent propanediol-utilizing BMC. Here we functionally and structurally characterize enzymes of the GRM of Rhodopseudomonas palustris BisB18 and demonstrate their concerted function in vitro. The GRM signature enzyme, the GRE, is a dedicated 1,2-propanediol dehydratase with a new type of intramolecular encapsulation peptide. It forms a complex with its activating enzyme and, in conjunction with an aldehyde dehydrogenase, converts 1,2-propanediol to propionyl-CoA. Notably, homologous GRMs are also encoded in pathogenic Escherichia coli strains. Our high-resolution crystal structures of the aldehyde dehydrogenase lead to a revised reaction mechanism. The successful in vitro reconstitution of a part of the GRM metabolism provides insights into the metabolic function and steps in the assembly of this BMC.

    Organizational Affiliation: 

    Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldehyde dehydrogenase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
524Rhodopseudomonas palustris BisB18Mutation(s): 0 
Gene Names: RPC_1174
UniProt
Find proteins for Q21A49 (Rhodopseudomonas palustris (strain BisB18))
Explore Q21A49 
Go to UniProtKB:  Q21A49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ21A49
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VU
Query on 1VU
Download Ideal Coordinates CCD File 
I [auth A],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
I [auth A],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
propionyl Coenzyme A
C24 H40 N7 O17 P3 S
QAQREVBBADEHPA-IEXPHMLFSA-N		 Ligand Interaction
COA
Query on COA
Download Ideal Coordinates CCD File 
J [auth B]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.106α = 89.52
b = 105.775β = 71
c = 126.425γ = 68.92
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release