5N9Z

Rubisco from Thalassiosira hyalina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 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:  
    5MZ2, 5N9Z, 5OYA, 6FTL

  • PubMed Abstract: 
  • 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 ...

    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, inger.andersson@icm.uu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chainA, I [auth B], K [auth C], G [auth D], M [auth E], E [auth F], O [auth G], C [auth H]490Thalassiosira hyalinaMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for A0A384E0M2 (Thalassiosira hyalina)
Explore A0A384E0M2 
Go to UniProtKB:  A0A384E0M2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunitB [auth I], L [auth J], N [auth K], P [auth L], H [auth M], F [auth N], D [auth O], J [auth P]139Thalassiosira hyalinaMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for A0A384E0M3 (Thalassiosira hyalina)
Explore A0A384E0M3 
Go to UniProtKB:  A0A384E0M3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP (Subject of Investigation/LOI)
Query on CAP

Download Ideal Coordinates CCD File 
DA [auth F], HA [auth D], MA [auth B], PA [auth C], R [auth A], TA [auth E], Y [auth H], ZA [auth G]2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth O] , AB [auth L] , BA [auth O] , EA [auth N] , IA [auth M] , JA [auth M] , KA [auth M] , NA [auth P] , 
AA [auth O], AB [auth L], BA [auth O], EA [auth N], IA [auth M], JA [auth M], KA [auth M], NA [auth P], QA [auth J], RA [auth J], S [auth A], U [auth I], UA [auth K], V [auth I], VA [auth K], W [auth I], WA [auth K], XA [auth K], Z [auth O]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth F] , FA [auth N] , GA [auth D] , LA [auth B] , OA [auth C] , Q [auth A] , SA [auth E] , T [auth I] , 
CA [auth F], FA [auth N], GA [auth D], LA [auth B], OA [auth C], Q [auth A], SA [auth E], T [auth I], X [auth H], YA [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  7 Unique
IDChainsTypeFormula2D DiagramParent
8RE
Query on 8RE
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC6 H14 N2 O4LYS
CSO
Query on CSO
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
HLU
Query on HLU
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC6 H13 N O3LEU
HYP
Query on HYP
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC7 H14 N2 O4LYS
LYO
Query on LYO
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC6 H14 N2 O3LYS
M3L
Query on M3L
A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.992α = 90
b = 219.986β = 118.34
c = 124.274γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
Omodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 2.0: 2019-04-24
    Changes: Data collection, Polymer sequence
  • Version 3.0: 2019-05-15
    Changes: Data collection, Polymer sequence