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PDBsum entry 2vdh

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2vdh
Jmol
Contents
Protein chains
(+ 2 more) 465 a.a. *
(+ 2 more) 140 a.a. *
Ligands
CAP ×8
EDO ×57
Metals
_MG ×8
Waters ×1800
* Residue conservation analysis
PDB id:
2vdh
Name: Lyase
Title: Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit c172s mutation
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a, b, c, d, e, f, g, h. Synonym: ribulose-1,5-bisphosphate carboxylase large chain, rubisco large subunit. Engineered: yes. Mutation: yes. Ribulose bisphosphate carboxylase small chain 1. Chain: i, j, k, l, m, n, o, p. Synonym: rubisco small subunit 1,ribulose-1,5-bisphosphate
Source: Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: 18-7g. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.172     R-free:   0.203
Authors: M.-J.Garcia-Murria,S.Karkehabadi,J.Marin-Navarro, S.Satagopan,I.Andersson,R.J.Spreitzer,J.Moreno
Key ref: M.J.García-Murria et al. (2008). Structural and functional consequences of the replacement of proximal residues Cys(172) and Cys(192) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii. Biochem J, 411, 241-247. PubMed id: 18072944 DOI: 10.1042/BJ20071422
Date:
09-Oct-07     Release date:   04-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
465 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 8 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: 10.1042/BJ20071422 Biochem J 411:241-247 (2008)
PubMed id: 18072944  
 
 
Structural and functional consequences of the replacement of proximal residues Cys(172) and Cys(192) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii.
M.J.García-Murria, S.Karkehabadi, J.Marín-Navarro, S.Satagopan, I.Andersson, R.J.Spreitzer, J.Moreno.
 
  ABSTRACT  
 
Proximal Cys(172) and Cys(192) in the large subunit of the photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) are evolutionarily conserved among cyanobacteria, algae and higher plants. Mutation of Cys(172) has been shown to affect the redox properties of Rubisco in vitro and to delay the degradation of the enzyme in vivo under stress conditions. Here, we report the effect of the replacement of Cys(172) and Cys(192) by serine on the catalytic properties, thermostability and three-dimensional structure of Chlamydomonas reinhardtii Rubisco. The most striking effect of the C172S substitution was an 11% increase in the specificity factor when compared with the wild-type enzyme. The specificity factor of C192S Rubisco was not altered. The V(c) (V(max) for carboxylation) was similar to that of wild-type Rubisco in the case of the C172S enzyme, but approx. 30% lower for the C192S Rubisco. In contrast, the K(m) for CO(2) and O(2) was similar for C192S and wild-type enzymes, but distinctly higher (approximately double) for the C172S enzyme. C172S Rubisco showed a critical denaturation temperature approx. 2 degrees C lower than wild-type Rubisco and a distinctly higher denaturation rate at 55 degrees C, whereas C192S Rubisco was only slightly more sensitive to temperature denaturation than the wild-type enzyme. X-ray crystal structures reveal that the C172S mutation causes a shift of the main-chain backbone atoms of beta-strand 1 of the alpha/beta-barrel affecting a number of amino acid side chains. This may cause the exceptional catalytic features of C172S. In contrast, the C192S mutation does not produce similar structural perturbations.