1UW9

L290F-A222T chlamydomonas Rubisco mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Altered Intersubunit Interactions in Crystal Structures of Catalytically Compromised Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Karkehabadi, S., Taylor, T.C., Spreitzer, R.J., Andersson, I.

(2005) Biochemistry 44: 113

  • DOI: 10.1021/bi047928e
  • Primary Citation of Related Structures:  
    1UW9, 1UWA

  • PubMed Abstract: 

    • Substitution of Leu290 by Phe (L290F) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from the unicellular green alga Chlamydomonas reinhardtii causes a 13% decrease in CO(2)/O(2) specificity and reduced thermal stability. Genetic selection for restored photosynthesis at the restrictive temperature identified an Ala222 to Thr (A222T) substitution that suppresses the deleterious effects of the original mutant substitution to produce a revertant enzyme with improved thermal stability and kinetic properties virtually indistinguishable from that of the wild-type enzyme ...

    Substitution of Leu290 by Phe (L290F) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from the unicellular green alga Chlamydomonas reinhardtii causes a 13% decrease in CO(2)/O(2) specificity and reduced thermal stability. Genetic selection for restored photosynthesis at the restrictive temperature identified an Ala222 to Thr (A222T) substitution that suppresses the deleterious effects of the original mutant substitution to produce a revertant enzyme with improved thermal stability and kinetic properties virtually indistinguishable from that of the wild-type enzyme. Because the mutated residues are situated approximately 19 A away from the active site, they must affect the relative rates of carboxylation and oxygenation in an indirect way. As a means for elucidating the role of such distant interactions in Rubisco catalysis and stability, we have determined the crystal structures of the L290F mutant and L290F/A222T revertant enzymes to 2.30 and 2.05 A resolution, respectively. Inspection of the structures reveals that the mutant residues interact via van der Waals contacts within the same large subunit (intrasubunit path, 15.2 A Calpha-Calpha) and also via a path involving a neighboring small subunit (intersubunit path, 18.7 A Calpha-Calpha). Structural analysis of the mutant enzymes identified regions (residues 50-72 of the small subunit and residues 161-164 and 259-264 of the large subunit) that show significant and systematically increased atomic temperature factors in the L290F mutant enzyme compared to wild type. These regions coincide with residues on the interaction paths between the L290F mutant and A222T suppressor sites and could explain the temperature-conditional phenotype of the L290F mutant strain. This suggests that alterations in subunit interactions will influence protein dynamics and, thereby, affect catalysis.

    Organizational Affiliation: 

    Department of Molecular Biology, Swedish University of Agricultural Sciences, BMC Box 590, 751 24 Uppsala, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN475Chlamydomonas reinhardtiiMutation(s): 2 
Gene Names: rbcL
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1140Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RBCS1, RBCS-1, CHLRE_02g120100v5, CHLREDRAFT_82986
EC: 4.1.1.39
UniProt
Find proteins for P00873 (Chlamydomonas reinhardtii)
Explore P00873 
Go to UniProtKB:  P00873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00873
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP
Download Ideal Coordinates CCD File 
AC [auth V],
GB [auth O],
IA [auth E],
IB [auth O],
R [auth A],
AC [auth V],
GB [auth O],
IA [auth E],
IB [auth O],
R [auth A],
RB [auth R],
TB [auth R],
Z [auth B]
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 B],
AB [auth K],
BA [auth B],
BB [auth K],
CA [auth B],
AA [auth B],
AB [auth K],
BA [auth B],
BB [auth K],
CA [auth B],
CB [auth K],
CC [auth V],
DA [auth B],
DB [auth K],
DC [auth V],
EA [auth B],
EB [auth M],
EC [auth V],
FA [auth C],
FB [auth M],
FC [auth V],
GA [auth C],
GC [auth V],
HC [auth W],
IC [auth W],
JA [auth E],
JB [auth O],
KA [auth E],
KB [auth O],
LA [auth E],
LB [auth O],
MA [auth E],
MB [auth O],
NA [auth E],
NB [auth O],
OB [auth O],
PA [auth H],
PB [auth P],
QA [auth H],
QB [auth P],
RA [auth H],
S [auth A],
SA [auth H],
T [auth A],
TA [auth H],
U [auth A],
UA [auth H],
UB [auth R],
V [auth A],
VA [auth I],
VB [auth R],
W [auth A],
WA [auth J],
WB [auth R],
X [auth A],
XA [auth J],
XB [auth R],
YB [auth T],
ZA [auth K],
ZB [auth T]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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BC [auth V],
HA [auth E],
HB [auth O],
OA [auth H],
Q [auth A],
BC [auth V],
HA [auth E],
HB [auth O],
OA [auth H],
Q [auth A],
SB [auth R],
Y [auth B],
YA [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A,
B,
D [auth E],
F [auth H],
I [auth K],
A,
B,
D [auth E],
F [auth H],
I [auth K],
K [auth O],
M [auth R],
O [auth V]
L-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX
A,
B,
D [auth E],
F [auth H],
I [auth K],
A,
B,
D [auth E],
F [auth H],
I [auth K],
K [auth O],
M [auth R],
O [auth V]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC
A,
B,
D [auth E],
F [auth H],
I [auth K],
A,
B,
D [auth E],
F [auth H],
I [auth K],
K [auth O],
M [auth R],
O [auth V]
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.073α = 90
b = 178.196β = 120.35
c = 120.463γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other