1UZH

A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Chimeric Small Subunits Influence Catalysis without Causing Global Conformational Changes in the Crystal Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Karkehabadi, S.Peddi, S.R.Anwaruzzaman, M.Taylor, T.C.Cederlund, A.Genkov, T.Andersson, I.Spreitzer, R.J.

(2005) Biochemistry 44: 9851

  • DOI: 10.1021/bi050537v
  • Primary Citation of Related Structures:  
    1UZH, 1UZD

  • PubMed Abstract: 
  • Comparison of subunit sequences and X-ray crystal structures of ribulose-1,5-bisphosphate carboxylase/oxygenase indicates that the loop between beta-strands A and B of the small subunit is one of the most variable regions of the holoenzyme. In prokar ...

    Comparison of subunit sequences and X-ray crystal structures of ribulose-1,5-bisphosphate carboxylase/oxygenase indicates that the loop between beta-strands A and B of the small subunit is one of the most variable regions of the holoenzyme. In prokaryotes and nongreen algae, the loop contains 10 residues. In land plants and green algae, the loop is comprised of approximately 22 and 28 residues, respectively. Previous studies indicated that the longer betaA-betaB loop was required for the assembly of cyanobacterial small subunits with plant large subunits in isolated chloroplasts. In the present study, chimeric small subunits were constructed by replacing the loop of the green alga Chlamydomonas reinhardtii with the sequences of Synechococcus or spinach. When these engineered genes were transformed into a Chlamydomonas mutant that lacks small-subunit genes, photosynthesis-competent colonies were recovered, indicating that loop size is not essential for holoenzyme assembly. Whereas the Synechococcus loop causes decreases in carboxylation V(max), K(m)(O(2)), and CO(2)/O(2) specificity, the spinach loop causes complementary decreases in carboxylation V(max), K(m)(O(2)), and K(m)(CO(2)) without a change in specificity. X-ray crystal structures of the engineered proteins reveal remarkable similarity between the introduced betaA-betaB loops and the respective loops in the Synechococcus and spinach enzymes. The side chains of several large-subunit residues are altered in regions previously shown by directed mutagenesis to influence CO(2)/O(2) specificity. Differences in the catalytic properties of divergent Rubisco enzymes may arise from differences in the small-subunit betaA-betaB loop. This loop may be a worthwhile target for genetic engineering aimed at improving photosynthetic CO(2) fixation.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAINA, B, E, H, K, O, R, V475Chlamydomonas reinhardtiiSynechococcus sp.
This entity is chimeric
Mutation(s): 0 
Gene Names: rbcL
EC: 4.1.1.39
Find proteins for P00877 (Chlamydomonas reinhardtii)
Explore P00877 
Go to UniProtKB:  P00877
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 CHAIN 2, RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAINC, F, I, J, M, P, T, W122Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RBCS-1CHLRE_02g120100v5CHLREDRAFT_82986
EC: 4.1.1.39
Find proteins for P04716 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P04716 
Go to UniProtKB:  P04716
Find proteins for P00873 (Chlamydomonas reinhardtii)
Explore P00873 
Go to UniProtKB:  P00873
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 CCD File 
A, B, E, H, K, O, R, V
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, E, F, H, J, K, M, O, P, R, T, V, W
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, E, H, K, O, R, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A,B,E,H,K,O,R,VL-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX
A,B,E,H,K,O,R,VL-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC
A,B,E,H,K,O,R,VL-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.82α = 90
b = 223.969β = 90
c = 111.752γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-31
    Type: Initial release
  • Version 1.1: 2011-05-07
    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
  • Version 1.4: 2019-12-18
    Changes: Other, Source and taxonomy, Structure summary
  • Version 1.5: 2020-07-29
    Changes: Derived calculations, Source and taxonomy