8BDB

Ribulose-1,5-bisphosphate carboxylase/oxygenase from Griffithsia monilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth.

Zhou, Y.Gunn, L.H.Birch, R.Andersson, I.Whitney, S.M.

(2023) Nat Plants 9: 978-986

  • DOI: https://doi.org/10.1038/s41477-023-01436-7
  • Primary Citation of Related Structures:  
    8BDB

  • PubMed Abstract: 

    Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 Å. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (k cat c ) by 60%, the carboxylation efficiency in air by 22% and the CO 2 /O 2 specificity (S c/o ) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.


  • Organizational Affiliation

    Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain
A, C, G, K, O
480Griffithsia monilisMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for A7UM67 (Griffithsia monilis)
Explore A7UM67 
Go to UniProtKB:  A7UM67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7UM67
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small chain
B, D, F, H, J
B, D, F, H, J, L, N, P
138Griffithsia monilisMutation(s): 0 
UniProt
Find proteins for A7UM68 (Griffithsia monilis)
Explore A7UM68 
Go to UniProtKB:  A7UM68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7UM68
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain
E, I, M
480Griffithsia monilisMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for A7UM67 (Griffithsia monilis)
Explore A7UM67 
Go to UniProtKB:  A7UM67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7UM67
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
EE [auth K]
IC [auth G]
ID [auth I]
NB [auth E]
R [auth A]
EE [auth K],
IC [auth G],
ID [auth I],
NB [auth E],
R [auth A],
RA [auth C],
TF [auth O],
ZE [auth M]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth C]
AD [auth H]
AE [auth J]
AF [auth M]
AA [auth A],
AB [auth C],
AD [auth H],
AE [auth J],
AF [auth M],
AG [auth O],
BA [auth A],
BB [auth C],
BD [auth H],
BE [auth J],
BF [auth M],
BG [auth O],
CA [auth A],
CB [auth C],
CC [auth F],
CD [auth H],
CE [auth J],
CF [auth M],
CG [auth O],
DA [auth A],
DC [auth F],
DD [auth H],
DF [auth M],
EA [auth A],
EC [auth F],
ED [auth H],
EF [auth M],
FB [auth D],
FC [auth F],
FD [auth H],
FE [auth K],
FF [auth M],
GB [auth D],
GC [auth F],
GE [auth K],
GF [auth M],
GG [auth P],
HB [auth D],
HE [auth K],
HG [auth P],
IB [auth D],
IE [auth K],
IG [auth P],
JA [auth B],
JB [auth D],
JC [auth G],
JD [auth I],
JE [auth K],
JG [auth P],
KA [auth B],
KB [auth D],
KC [auth G],
KD [auth I],
KE [auth K],
KF [auth N],
KG [auth P],
LA [auth B],
LC [auth G],
LD [auth I],
LE [auth K],
LF [auth N],
LG [auth P],
MA [auth B],
MC [auth G],
MD [auth I],
ME [auth K],
MF [auth N],
MG [auth P],
NA [auth B],
NC [auth G],
ND [auth I],
NF [auth N],
NG [auth P],
OA [auth B],
OB [auth E],
OC [auth G],
OD [auth I],
OF [auth N],
PB [auth E],
PC [auth G],
PD [auth I],
PE [auth L],
PF [auth N],
QB [auth E],
QC [auth G],
QD [auth I],
QE [auth L],
QF [auth N],
RB [auth E],
RC [auth G],
RD [auth I],
RE [auth L],
S [auth A],
SA [auth C],
SB [auth E],
SC [auth G],
SD [auth I],
SE [auth L],
T [auth A],
TA [auth C],
TB [auth E],
TC [auth G],
TD [auth I],
TE [auth L],
U [auth A],
UA [auth C],
UB [auth E],
UE [auth L],
UF [auth O],
V [auth A],
VA [auth C],
VB [auth E],
VE [auth L],
VF [auth O],
W [auth A],
WA [auth C],
WB [auth E],
WE [auth L],
WF [auth O],
X [auth A],
XA [auth C],
XB [auth E],
XD [auth J],
XF [auth O],
Y [auth A],
YA [auth C],
YD [auth J],
YF [auth O],
Z [auth A],
ZA [auth C],
ZC [auth H],
ZD [auth J],
ZF [auth O]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

Download Ideal Coordinates CCD File 
AC [auth E]
BC [auth E]
DB [auth C]
DG [auth O]
EB [auth C]
AC [auth E],
BC [auth E],
DB [auth C],
DG [auth O],
EB [auth C],
EG [auth O],
FA [auth A],
FG [auth O],
GA [auth A],
GD [auth H],
HA [auth A],
HF [auth M],
IA [auth A],
IF [auth M],
JF [auth M],
LB [auth D],
NE [auth K],
OE [auth K],
PA [auth B],
RF [auth N],
UC [auth G],
UD [auth I],
VC [auth G],
VD [auth I],
WC [auth G],
WD [auth I],
XC [auth G],
XE [auth L],
YB [auth E],
YC [auth G],
ZB [auth E]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
DE [auth K]
HC [auth G]
HD [auth I]
MB [auth E]
Q [auth A]
DE [auth K],
HC [auth G],
HD [auth I],
MB [auth E],
Q [auth A],
QA [auth C],
SF [auth O],
YE [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
CCS
Query on CCS
A, C, G, K, O
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
HL2
Query on HL2
A, C, G, K, O
L-PEPTIDE LINKINGC6 H13 N O3LEU
KCX
Query on KCX
A, C, G, K, O
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.328α = 90
b = 131.925β = 94.75
c = 196.319γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2015-05007

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2023-06-28
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description