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PDBsum entry 3axk

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
3axk
Jmol
Contents
Protein chains
434 a.a.
121 a.a.
Ligands
GOL ×4
NDP ×2
Metals
_MG ×2
Waters ×1125
PDB id:
3axk
Name: Lyase
Title: Structure of rice rubisco in complex with NADP(h)
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a, b. Synonym: rubisco large subunit, d-ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit. Ribulose bisphosphate carboxylase small chain, chloroplastic. Chain: s, t. Synonym: rubisco small subunit, d-ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit.
Source: Oryza sativa japonica group. Japanese rice. Organism_taxid: 39947. Tissue: leaves. Tissue: leaves
Resolution:
1.90Å     R-factor:   0.169     R-free:   0.189
Authors: H.Matsumura,E.Mizohata,H.Ishida,A.Kogami,T.Ueno,A.Makino,T.I A.Yokota,T.Mae,Y.Kai
Key ref: H.Matsumura et al. (2012). Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate. J Mol Biol, 422, 75-86. PubMed id: 22609438
Date:
11-Apr-11     Release date:   11-Apr-12    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0C512  (RBL_ORYSJ) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
477 a.a.
434 a.a.*
Protein chains
Pfam   ArchSchema ?
Q0INY7  (RBS1_ORYSJ) -  Ribulose bisphosphate carboxylase small chain, chloroplastic
Seq:
Struc:
175 a.a.
121 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, S, B, T: 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    
 
 
J Mol Biol 422:75-86 (2012)
PubMed id: 22609438  
 
 
Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate.
H.Matsumura, E.Mizohata, H.Ishida, A.Kogami, T.Ueno, A.Makino, T.Inoue, A.Yokota, T.Mae, Y.Kai.
 
  ABSTRACT  
 
No abstract given.