6KYJ

Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfate ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C 4 Plant-like High Catalytic Activity.

Matsumura, H.Shiomi, K.Yamamoto, A.Taketani, Y.Kobayashi, N.Yoshizawa, T.Tanaka, S.I.Yoshikawa, H.Endo, M.Fukayama, H.

(2020) Mol Plant 13: 1570-1581

  • DOI: 10.1016/j.molp.2020.08.012
  • Primary Citation of Related Structures:  
    6KYI, 6KYJ

  • PubMed Abstract: 
  • Photosynthetic rate at the present atmospheric condition is limited by the CO 2 -fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) because of its extremely low catalytic rate (k cat ) and poor affinity for CO 2 (K c ) and specificity for CO 2 (S c/o ) ...

    Photosynthetic rate at the present atmospheric condition is limited by the CO 2 -fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) because of its extremely low catalytic rate (k cat ) and poor affinity for CO 2 (K c ) and specificity for CO 2 (S c/o ). Rubisco in C 4 plants generally shows higher k cat than that in C 3 plants. Rubisco consists of eight large subunits and eight small subunits (RbcS). Previously, the chimeric incorporation of sorghum C 4 -type RbcS significantly increased the k cat of Rubisco in a C 3 plant, rice. In this study, we knocked out rice RbcS multigene family using the CRISPR-Cas9 technology and completely replaced rice RbcS with sorghum RbcS in rice Rubisco. Obtained hybrid Rubisco showed almost C 4 plant-like catalytic properties, i.e., higher k cat , higher K c , and lower S c/o . Transgenic lines expressing the hybrid Rubisco accumulated reduced levels of Rubisco, whereas they showed slightly but significantly higher photosynthetic capacity and similar biomass production under high CO 2 condition compared with wild-type rice. High-resolution crystal structural analysis of the wild-type Rubisco and hybrid Rubisco revealed the structural differences around the central pore of Rubisco and the βC-βD hairpin in RbcS. We propose that such differences, particularly in the βC-βD hairpin, may impact the flexibility of Rubisco catalytic site and change its catalytic properties.


    Organizational Affiliation

    Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-tyou, Nada-ku, Kobe 657-8501, Japan. Electronic address: fukayama@people.kobe-u.ac.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chainA, E [auth C], C [auth E], G477Oryza sativaMutation(s): 0 
Gene Names: rbcLPA064
EC: 4.1.1.39
UniProt
Find proteins for P0C510 (Oryza sativa)
Explore P0C510 
Go to UniProtKB:  P0C510
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small chainB [auth S], F [auth U], D [auth W], H [auth Y]169Sorghum bicolorMutation(s): 0 
Gene Names: RbcS
EC: 4.1.1.39
UniProt
Find proteins for E3WDK7 (Sorghum bicolor)
Explore E3WDK7 
Go to UniProtKB:  E3WDK7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , HA [auth G] , I [auth A] , IA [auth G] , J [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  HA [auth G],  I [auth A],  IA [auth G],  J [auth A],  JA [auth G],  K [auth A],  KA [auth G],  L [auth A],  LA [auth G],  M [auth A],  N [auth A],  R [auth E],  S [auth E],  T [auth E],  U [auth E],  V [auth E],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth C] , FA [auth C] , GA [auth C] , MA [auth G] , NA [auth G] , O [auth A] , OA [auth G] , P [auth A] , 
EA [auth C],  FA [auth C],  GA [auth C],  MA [auth G],  NA [auth G],  O [auth A],  OA [auth G],  P [auth A],  PA [auth G],  Q [auth A],  W [auth E],  X [auth E],  Y [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.79α = 90
b = 223.79β = 90
c = 108.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19K07582
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H04735
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18K06094
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H05732

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references