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PDBsum entry 4f0m

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protein ligands metals links
Lyase PDB id
4f0m
Jmol
Contents
Protein chains
448 a.a.
138 a.a.
Ligands
GOL ×3
Metals
_MG
_CL
Waters ×353
PDB id:
4f0m
Name: Lyase
Title: Unactivated rubisco with magnesium and a water molecule boun
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a. Synonym: rubisco large subunit. Ribulose bisphosphate carboxylase small chain. Chain: b. Synonym: rubisco small subunit. Ec: 4.1.1.39
Source: Galdieria sulphuraria. Red alga. Organism_taxid: 130081. Organism_taxid: 130081
Resolution:
2.25Å     R-factor:   0.163     R-free:   0.234
Authors: B.Stec
Key ref: B.Stec (2012). Structural mechanism of RuBisCO activation by carbamylation of the active site lysine. Proc Natl Acad Sci U S A, 109, 18785-18790. PubMed id: 23112176 DOI: 10.1073/pnas.1210754109
Date:
04-May-12     Release date:   14-Nov-12    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23755  (RBL_GALSU) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
493 a.a.
448 a.a.*
Protein chain
Pfam   ArchSchema ?
P23756  (RBS_GALSU) -  Ribulose bisphosphate carboxylase small chain
Seq:
Struc:
138 a.a.
138 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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
Bound ligand (Het Group name = GOL)
matches with 54.55% similarity
+ 2 × H(+)
= D-ribulose 1,5-bisphosphate
+ CO(2)
+ 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: 10.1073/pnas.1210754109 Proc Natl Acad Sci U S A 109:18785-18790 (2012)
PubMed id: 23112176  
 
 
Structural mechanism of RuBisCO activation by carbamylation of the active site lysine.
B.Stec.
 
  ABSTRACT  
 
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO(2). We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O(2) and CO(2) bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO(2) defines an elusive, preactivation complex that contains a metal cation Mg(2+) surrounded by three H(2)O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming.