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PDBsum entry 1upp

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1upp
Jmol
Contents
Protein chains
467 a.a.
123 a.a. *
Ligands
CAP ×4
Metals
_CA ×4
Waters ×664
* Residue conservation analysis
PDB id:
1upp
Name: Lyase
Title: Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium.
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a, c, e, g. Synonym: ribulose bisphosphate carboxylase/oxygenase, rubisco large subunit. Ribulose bisphosphate carboxylase small chain. Chain: i, j, k, l. Synonym: ribulose bisphosphate carboxylase/oxygenase, rubisco small subunit. Other_details: this is the second structure of this
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Organ: leaf. Organ: leaf
Biol. unit: 60mer (from PDB file)
Resolution:
2.3Å     R-factor:   0.258     R-free:   0.307
Authors: S.Karkehabadi,T.C.Taylor,I.Andersson
Key ref:
S.Karkehabadi et al. (2003). Calcium supports loop closure but not catalysis in Rubisco. J Mol Biol, 334, 65-73. PubMed id: 14596800 DOI: 10.1016/j.jmb.2003.09.025
Date:
09-Oct-03     Release date:   14-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00875  (RBL_SPIOL) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
467 a.a.*
Protein chains
Pfam   ArchSchema ?
Q43832  (RBS2_SPIOL) -  Ribulose bisphosphate carboxylase small chain 2, chloroplastic
Seq:
Struc:
180 a.a.
123 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, C, E, G, I, J, K, L: 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)
+ 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.2003.09.025 J Mol Biol 334:65-73 (2003)
PubMed id: 14596800  
 
 
Calcium supports loop closure but not catalysis in Rubisco.
S.Karkehabadi, T.C.Taylor, I.Andersson.
 
  ABSTRACT  
 
Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses CO(2) assimilation in biology. A prerequisite for catalysis is an activation process, whereby an active site lysine is selectively carbamylated. The carbamyl group is then stablised by a metal ion, which in vivo is Mg(2+). Other divalent metal ions can replace Mg(2+) as activators in vitro, but the nature of the metal ion strongly influences the catalytic activity of the enzyme and has a differential effect on the ratio of the carboxylation reaction and the competing oxygenation reaction. Biochemical studies show that calcium promotes carbamylation but not catalysis. To investigate the role of the metal in catalysis, we have determined two structures of the enzyme complexed with Ca(2+) and the transition state analogue 2-carboxy-D-arbinitol-1,5-bisphosphate (2CABP). One of the complexes was prepared by soaking 2CABP into crystals of the enzyme-Ca(2+)-product complex, while the other was obtained by cocrystallising the enzyme with calcium and 2CABP under activating conditions. The two crystals belong to different space groups, and one was merohedrally twinned. Both complexes show very similar three-dimensional features. The enzyme is carbamylated at Lys201, and requisite loops close over the bound ligands in the active site, shielding them from the solvent in a manner similar to the corresponding complex with Mg(2+). However, there are subtle differences that could explain the particular role of Ca(2+) in these processes. The larger radius of the calcium ion and its reduced Lewis-acid character causes a significant increase in the required proton hop distance between the C3 proton and the carbamate on Lys201 in the calcium complex. This alone could explain the inability of calcium to sustain catalysis in Rubisco. Similar effects are also expected on subsequent proton transfer steps in the catalytic cycle. Here we also discuss the effect of metal substitution on the dynamics of the ligands around the metal ion.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Comparison of the structures of Rubisco-Ca^2+-2CABP (C atoms coloured yellow) and Rubisco-Ca^2+-RuBP (C atoms coloured green) in the region around loop 6 of the a/b-barrel. In the Rubisco-Ca^2+-RuBP complex, loop 6 is retracted from the active site and Lys334 makes no interactions with the substrate.
Figure 3.
Figure 3. Comparison of the structures of Rubisco-Ca^2+-2CABP complex (in yellow) and Rubisco-Mg2+-2CABP complex (in red).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 65-73) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23385454 R.J.Read, P.D.Adams, and A.J.McCoy (2013).
Intensity statistics in the presence of translational noncrystallographic symmetry.
  Acta Crystallogr D Biol Crystallogr, 69, 176-183.  
19837658 H.Alonso, M.J.Blayney, J.L.Beck, and S.M.Whitney (2009).
Substrate-induced assembly of Methanococcoides burtonii D-ribulose-1,5-bisphosphate carboxylase/oxygenase dimers into decamers.
  J Biol Chem, 284, 33876-33882.  
18094473 P.H.Zwart, R.W.Grosse-Kunstleve, A.A.Lebedev, G.N.Murshudov, and P.D.Adams (2008).
Surprises and pitfalls arising from (pseudo)symmetry.
  Acta Crystallogr D Biol Crystallogr, 64, 99.  
16369097 A.A.Lebedev, A.A.Vagin, and G.N.Murshudov (2006).
Intensity statistics in twinned crystals with examples from the PDB.
  Acta Crystallogr D Biol Crystallogr, 62, 83-95.  
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.

 

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