6RQA

Crystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 general ...

    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

    LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany. toerb@mpi-marburg.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
iminosuccinate reductaseAB341Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: Pden_3918bhcD
EC: 1.4.1
Find proteins for A1B8Z0 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B8Z0 
Go to UniProtKB:  A1B8Z0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
7MT
Query on 7MT

Download CCD File 
B
Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
TB
Query on TB

Download CCD File 
A
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.386α = 90
b = 72.407β = 90
c = 164.266γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB987
European UnionGermanyFET686330

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Database references