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PDBsum entry 1rlc

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protein ligands Protein-protein interface(s) links
Lyase(carbon-carbon) PDB id
1rlc
Jmol
Contents
Protein chains
441 a.a.
123 a.a. *
Ligands
CAP
* Residue conservation analysis
PDB id:
1rlc
Name: Lyase(carbon-carbon)
Title: Crystal structure of the unactivated ribulose 1, 5-bisphosph carboxylase(slash)oxygenase complexed with a transition sta 2-carboxy-d-arabinitol 1,5-bisphosphate
Structure: Ribulose 1,5 bisphosphate carboxylase/oxygenase ( chain). Chain: l. Engineered: yes. Ribulose 1,5 bisphosphate carboxylase/oxygenase ( chain). Chain: s. Engineered: yes
Source: Nicotiana tabacum. Common tobacco. Organism_taxid: 4097. Organism_taxid: 4097
Biol. unit: 60mer (from PQS)
Resolution:
2.70Å     R-factor:   0.196    
Authors: K.Y.J.Zhang,D.Cascio,D.Eisenberg
Key ref: K.Y.Zhang et al. (1994). Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate. Protein Sci, 3, 64-69. PubMed id: 8142899 DOI: 10.1002/pro.5560030109
Date:
04-Aug-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00876  (RBL_TOBAC) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
477 a.a.
441 a.a.
Protein chain
Pfam   ArchSchema ?
P69249  (RBS_TOBAC) -  Ribulose bisphosphate carboxylase small chain, chloroplastic
Seq:
Struc:
180 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains L, S: 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: 10.1002/pro.5560030109 Protein Sci 3:64-69 (1994)
PubMed id: 8142899  
 
 
Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.
K.Y.Zhang, D.Cascio, D.Eisenberg.
 
  ABSTRACT  
 
The crystal structure of unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate, was determined to 2.7 A resolution by X-ray crystallography. The transition state analog binds at the active site in an extended conformation. As compared to the binding of the same analog in the activated enzyme, the analog binds in a reverse orientation. The active site Lys 201 is within hydrogen bonding distance of the carboxyl oxygen of the analog. Loop 6 (residues 330-339) remains open and flexible upon binding of the analog in the unactivated enzyme, in contrast to the closed and ordered loop 6 in the activated enzyme complex. The transition state analog is exposed to solvent due to the open conformation of loop 6.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19690372 H.Tamura, Y.Saito, H.Ashida, Y.Kai, T.Inoue, A.Yokota, and H.Matsumura (2009).
Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 65, 942-951.
PDB code: 2zvi
18487131 F.R.Tabita, T.E.Hanson, S.Satagopan, B.H.Witte, and N.E.Kreel (2008).
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms.
  Philos Trans R Soc Lond B Biol Sci, 363, 2629-2640.  
16763877 B.Balaji, M.Gilson, and H.Roy (2006).
Binding of a transition state analog to newly synthesized Rubisco.
  Photosynth Res, 89, 43-48.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.