Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

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Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.

Schada von Borzyskowski, L.Severi, F.Kruger, K.Hermann, L.Gilardet, A.Sippel, F.Pommerenke, B.Claus, P.Cortina, N.S.Glatter, T.Zauner, S.Zarzycki, J.Fuchs, B.M.Bremer, E.Maier, U.G.Amann, R.I.Erb, T.J.

(2019) Nature 575: 500-504

  • DOI: https://doi.org/10.1038/s41586-019-1748-4
  • Primary Citation of Related Structures:  
    6QKB, 6RQA

  • PubMed Abstract: 

    One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments 1 . Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria 2-4 , the further fate of this C 2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the β-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago 5 . We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing-to our knowledge-the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.

  • Organizational Affiliation

    Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. schada@mpi-marburg.mpg.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-3-hydroxyaspartate aldolase
A, B
387Paracoccus denitrificansMutation(s): 0 
Gene Names: Pden_3919
EC: 4.1.3
Find proteins for A1B8Z1 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B8Z1 
Go to UniProtKB:  A1B8Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B8Z1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.598α = 90
b = 75.247β = 90
c = 157.31γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB987
European UnionGermanyFET686330

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2019-12-04
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description