spacer
spacer

PDBsum entry 1wdd

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1wdd
Jmol
Contents
Protein chains
465 a.a. *
122 a.a. *
Ligands
CAP ×2
GOL ×17
Metals
_MG ×2
Waters ×999
* Residue conservation analysis
PDB id:
1wdd
Name: Lyase
Title: Crystal structure of activated rice rubisco complexed with 2 carboxyarabinitol-1,5-bisphosphate
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a, e. Synonym: large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, rubisco large subunit. Ribulose bisphosphate carboxylase small chain c. Chain: s, w. Synonym: small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, rubisco small subunit c. Ec: 4.1.1.39
Source: Oryza sativa japonica group. Japanese rice. Organism_taxid: 39947. Tissue: leaves. Tissue: leaves
Biol. unit: 60mer (from PDB file)
Resolution:
1.35Å     R-factor:   0.160     R-free:   0.182
Authors: E.Mizohata,H.Matsumura,T.Ueno,H.Ishida,T.Inoue,A.Makino,T.Ma
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 DOI: 10.1016/j.jmb.2012.05.014
Date:
13-May-04     Release date:   13-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0C512  (RBL_ORYSJ) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
477 a.a.
465 a.a.*
Protein chains
Pfam   ArchSchema ?
Q0INY7  (RBS1_ORYSJ) -  Ribulose bisphosphate carboxylase small chain, chloroplastic
Seq:
Struc:
175 a.a.
122 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, S, E, W: 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 85.71% similarity
+ 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: 10.1016/j.jmb.2012.05.014 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.