6FTL

Rubisco from Skeletonema marinoi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.

Valegard, K.Andralojc, P.J.Haslam, R.P.Pearce, F.G.Eriksen, G.K.Madgwick, P.J.Kristoffersen, A.K.van Lun, M.Klein, U.Eilertsen, H.C.Parry, M.A.J.Andersson, I.

(2018) J. Biol. Chem. 293: 13033-13043

  • DOI: 10.1074/jbc.RA118.003518
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catalytic performance of the major CO <sub>2 </sub>-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibil ...

    The catalytic performance of the major CO 2 -assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO 2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from arctic waters were collected, cultivated, and analyzed for their CO 2 -fixing capability. We characterized the kinetic properties of five and determined the crystal structures of four Rubiscos selected for their high CO 2 -fixing efficiency. The DNA sequences of the rbc L and rbc S genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The V max and K m for the oxygenase and carboxylase activities at 25 °C and the specificity factors ( S c/o ) at 15, 25, and 35 °C were determined. The S c/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO 2 relative to O 2 Structurally, diatom Rubiscos belong to form I C/D, containing small subunits characterized by a short βA-βB loop and a C-terminal extension that forms a β-hairpin structure (βE-βF loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxyproline, β-hydroxyleucine, hydroxylated and nitrosylated cysteine, mono- and dihydroxylated lysine, and trimethylated lysine. Our studies suggest adaptation toward achieving efficient CO 2 fixation in arctic diatom Rubiscos.


    Organizational Affiliation

    From the Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden.,the Norwegian College of Fisheries Science, Arctic University of Norway, N-9037 Tromsø, Norway, and.,Department of Plant Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom.,the Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norway.,From the Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden, inger.andersson@icm.uu.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase large chain
A, C, E, G
484Skeletonema marinoiMutation(s): 0 
EC: 4.1.1.39
Find proteins for A0A3B6UEX0 (Skeletonema marinoi)
Go to UniProtKB:  A0A3B6UEX0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
I, J, K, L
139Skeletonema marinoiMutation(s): 0 
Find proteins for A0A3B6UEX1 (Skeletonema marinoi)
Go to UniProtKB:  A0A3B6UEX1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
C, E, G, I, J, K, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAP
Query on CAP

Download SDF File 
Download CCD File 
A, C, E, G
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A, C, E, G
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
KCX
Query on KCX
A, C, E, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
HYP
Query on HYP
A, C, E, G
L-PEPTIDE LINKINGC5 H9 N O3PRO
LYO
Query on LYO
A, C, E, G
L-PEPTIDE LINKINGC6 H14 N2 O3LYS
LOH
Query on LOH
A, C, E, G
NON-POLYMERC6 H14 N2 O4

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HLU
Query on HLU
A, C, E, G
L-PEPTIDE LINKINGC6 H13 N O3LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.022α = 90.00
b = 111.022β = 90.00
c = 396.361γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionSwedenQLK3-CT-2002-01945
FormasSweden--

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references
  • Version 1.2: 2018-09-05
    Type: Data collection, Database references
  • Version 1.3: 2019-04-17
    Type: Data collection, Structure summary
  • Version 2.0: 2019-04-24
    Type: Data collection, Polymer sequence