1IR2

Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.

Mizohata, E.Matsumura, H.Okano, Y.Kumei, M.Takuma, H.Onodera, J.Kato, K.Shibata, N.Inoue, T.Yokota, A.Kai, Y.

(2002) J Mol Biol 316: 679-691

  • DOI: https://doi.org/10.1006/jmbi.2001.5381
  • Primary Citation of Related Structures:  
    1IR1, 1IR2

  • PubMed Abstract: 

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyzes the initial steps of photosynthetic carbon reduction and photorespiratory carbon oxidation cycles by combining CO(2) and O(2), respectively, with ribulose-1,5-bisphosphate. Many photosynthetic organisms have form I rubiscos comprised of eight large (L) and eight small (S) subunits. The crystal structure of the complex of activated rubisco from the green alga Chlamydomonas reinhardtii and the reaction intermediate analogue 2-carboxyarabinitol-1,5-bisphosphate (2-CABP) has been solved at 1.84 A resolution (R(cryst) of 15.2 % and R(free) of 18.1 %). The subunit arrangement of Chlamydomonas rubisco is the same as those of the previously solved form I rubiscos. Especially, the present structure is very similar to the activated spinach structure complexed with 2-CABP in the L-subunit folding and active-site conformation, but differs in S-subunit folding. The central insertion of the Chlamydomonas S-subunit forms the longer betaA-betaB loop that protrudes deeper into the solvent channel of rubisco than higher plant, cyanobacterial, and red algal (red-like) betaA-betaB loops. The C-terminal extension of the Chlamydomonas S-subunit does not protrude into the solvent channel, unlike that of the red algal S-subunit, but lies on the protein surface anchored by interactions with the N-terminal region of the S-subunit. Further, the present high-resolution structure has revealed novel post-translational modifications. Residue 1 of the S-subunit is N(alpha)-methylmethionine, residues 104 and 151 of the L-subunit are 4-hydroxyproline, and residues 256 and 369 of the L-subunit are S(gamma)-methylcysteine. Furthermore, the unusual electron density of residue 471 of the L-subunit, which has been deduced to be threonine from the genomic DNA sequence, suggests that the residue is isoleucine produced by RNA editing or O(gamma)-methylthreonine.


  • Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large subunit of Rubisco475Chlamydomonas reinhardtiiMutation(s): 5 
EC: 4.1.1.39
UniProt
Find proteins for P00877 (Chlamydomonas reinhardtii)
Explore P00877 
Go to UniProtKB:  P00877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00877
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small subunit of Rubisco140Chlamydomonas reinhardtiiMutation(s): 1 
EC: 4.1.1.39
UniProt
Find proteins for P08475 (Chlamydomonas reinhardtii)
Explore P08475 
Go to UniProtKB:  P08475
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08475
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
AC [auth U]
DB [auth F]
EC [auth V]
HA [auth A]
HB [auth G]
AC [auth U],
DB [auth F],
EC [auth V],
HA [auth A],
HB [auth G],
IC [auth W],
LA [auth B],
MB [auth H],
MC [auth X],
QA [auth C],
RB [auth S],
RC [auth Y],
UA [auth D],
WB [auth T],
WC [auth Z],
YA [auth E]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth E]
BB [auth E]
BC [auth U]
CC [auth U]
EB [auth F]
AB [auth E],
BB [auth E],
BC [auth U],
CC [auth U],
EB [auth F],
FB [auth F],
FC [auth V],
GC [auth V],
IA [auth A],
IB [auth G],
JA [auth A],
JB [auth G],
JC [auth W],
KB [auth G],
KC [auth W],
MA [auth B],
NA [auth B],
NB [auth H],
NC [auth X],
OA [auth B],
OB [auth H],
OC [auth X],
PB [auth H],
PC [auth X],
RA [auth C],
SA [auth C],
SB [auth S],
SC [auth Y],
TB [auth S],
TC [auth Y],
UB [auth S],
UC [auth Y],
VA [auth D],
WA [auth D],
XB [auth T],
XC [auth Z],
YB [auth T],
YC [auth Z],
ZA [auth E],
ZC [auth Z]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CB [auth F]
DC [auth V]
GA [auth A]
GB [auth G]
HC [auth W]
CB [auth F],
DC [auth V],
GA [auth A],
GB [auth G],
HC [auth W],
KA [auth B],
LB [auth H],
LC [auth X],
PA [auth C],
QB [auth S],
QC [auth Y],
TA [auth D],
VB [auth T],
VC [auth Z],
XA [auth E],
ZB [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A
AA [auth X]
C [auth B]
CA [auth Y]
E [auth C]
A,
AA [auth X],
C [auth B],
CA [auth Y],
E [auth C],
EA [auth Z],
G [auth D],
I [auth E],
K [auth F],
M [auth G],
O [auth H],
Q [auth S],
S [auth T],
U,
W [auth V],
Y [auth W]
L-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX
A
AA [auth X]
C [auth B]
CA [auth Y]
E [auth C]
A,
AA [auth X],
C [auth B],
CA [auth Y],
E [auth C],
EA [auth Z],
G [auth D],
I [auth E],
K [auth F],
M [auth G],
O [auth H],
Q [auth S],
S [auth T],
U,
W [auth V],
Y [auth W]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC
A
AA [auth X]
C [auth B]
CA [auth Y]
E [auth C]
A,
AA [auth X],
C [auth B],
CA [auth Y],
E [auth C],
EA [auth Z],
G [auth D],
I [auth E],
K [auth F],
M [auth G],
O [auth H],
Q [auth S],
S [auth T],
U,
W [auth V],
Y [auth W]
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
MME
Query on MME
B [auth I]
BA [auth 6]
D [auth J]
DA [auth 7]
F [auth K]
B [auth I],
BA [auth 6],
D [auth J],
DA [auth 7],
F [auth K],
FA [auth 8],
H [auth L],
J [auth M],
L [auth N],
N [auth O],
P,
R [auth 1],
T [auth 2],
V [auth 3],
X [auth 4],
Z [auth 5]
L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.17α = 90
b = 174.75β = 97.75
c = 222.27γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-01-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection