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PDBsum entry 2v68

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2v68
Jmol
Contents
Protein chains
(+ 2 more) 466 a.a. *
(+ 2 more) 140 a.a. *
Ligands
EDO ×49
CAP ×8
Metals
_MG ×8
Waters ×2276
* Residue conservation analysis
PDB id:
2v68
Name: Oxidoreductase
Title: Crystal structure of chlamydomonas reinhardtii rubisco with large-subunit mutations v331a, t342i
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a, b, c, d, e, f, g, h. Synonym: rubisco large subunit, ribulose-1,5-bisphosphate carboxylase large chain. Engineered: yes. Mutation: yes. Ribulose bisphosphate carboxylase small chain 1. Chain: i, j, k, l, m, n, o, p. Fragment: residues 46-185.
Source: Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: 2137. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Resolution:
2.30Å     R-factor:   0.174     R-free:   0.203
Authors: S.Karkehabadi,S.Satagopan,T.C.Taylor,R.J.Spreitzer, I.Andersson
Key ref: S.Karkehabadi et al. (2007). Structural analysis of altered large-subunit loop-6/carboxy-terminus interactions that influence catalytic efficiency and CO2/O2 specificity of ribulose-1,5-bisphosphate carboxylase/oxygenase. Biochemistry, 46, 11080-11089. PubMed id: 17824672 DOI: 10.1021/bi701063f
Date:
13-Jul-07     Release date:   07-Aug-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
466 a.a.*
Protein chains
Pfam   ArchSchema ?
P00873  (RBS1_CHLRE) -  Ribulose bisphosphate carboxylase small chain 1, chloroplastic
Seq:
Struc:
185 a.a.
140 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.4.1.1.39  - Ribulose-bisphosphate carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
2 × 3-phospho-D-glycerate
+ 2 × H(+)
=
D-ribulose 1,5-bisphosphate
Bound ligand (Het Group name = CAP)
matches with 85.00% similarity
+
CO(2)
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plastid   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi701063f Biochemistry 46:11080-11089 (2007)
PubMed id: 17824672  
 
 
Structural analysis of altered large-subunit loop-6/carboxy-terminus interactions that influence catalytic efficiency and CO2/O2 specificity of ribulose-1,5-bisphosphate carboxylase/oxygenase.
S.Karkehabadi, S.Satagopan, T.C.Taylor, R.J.Spreitzer, I.Andersson.
 
  ABSTRACT  
 
The loop between alpha-helix 6 and beta-strand 6 in the alpha/beta-barrel of ribulose-1,5-bisphosphate carboxylase/oxygenase plays a key role in discriminating between CO2 and O2. Genetic screening in Chlamydomonas reinhardtii previously identified a loop-6 V331A substitution that decreases carboxylation and CO2/O2 specificity. Revertant selection identified T342I and G344S substitutions that restore photosynthetic growth by increasing carboxylation and specificity of the V331A enzyme. In numerous X-ray crystal structures, loop 6 is closed or open depending on the activation state of the enzyme and the presence or absence of ligands. The carboxy terminus folds over loop 6 in the closed state. To study the molecular basis for catalysis, directed mutagenesis and chloroplast transformation were used to create T342I and G344S substitutions alone. X-ray crystal structures were then solved for the V331A, V331A/T342I, T342I, and V331A/G344S enzymes, as well as for a D473E enzyme created to assess the role of the carboxy terminus in loop-6 closure. V331A disturbs a hydrophobic pocket, abolishing several van der Waals interactions. These changes are complemented by T342I and G344S, both of which alone cause decreases in CO2/O2 specificity. In the V331A/T342I revertant enzyme, Arg339 main-chain atoms are displaced. In V331A/G344S, alpha-helix 6 is shifted. D473E causes disorder of the carboxy terminus, but loop 6 remains closed. Interactions between a transition-state analogue and several residues are altered in the mutant enzymes. However, active-site Lys334 at the apex of loop 6 has a normal conformation. A variety of subtle interactions must be responsible for catalytic efficiency and CO2/O2 specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19705820 S.Satagopan, S.S.Scott, T.G.Smith, and F.R.Tabita (2009).
A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration.
  Biochemistry, 48, 9076-9083.  
18695049 P.A.Christin, N.Salamin, A.M.Muasya, E.H.Roalson, F.Russier, and G.Besnard (2008).
Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis.
  Mol Biol Evol, 25, 2361-2368.  
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