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PDBsum entry 1uzh

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1uzh
Jmol
Contents
Protein chains
(+ 2 more) 465 a.a. *
(+ 2 more) 122 a.a. *
Ligands
CAP ×8
EDO ×50
Metals
_MG ×8
Waters ×2831
* Residue conservation analysis
PDB id:
1uzh
Name: Lyase
Title: A chimeric chlamydomonas, synechococcus rubisco enzyme
Structure: Ribulose bisphosphate carboxylase large chain. Chain: a, b, e, h, k, o, r, v. Synonym: rubisco large subunit, ribulose-1,5 bisphosphate carboxylase large chain. Ribulose bisphosphate carboxylase small chain 2, ribulose bisphosphate carboxylase small chain. Chain: i, c, f, j, p, t, m, w. Synonym: rubisco small subunit 1,chloroplast, rubisco small subunit 2,oxygenase, ribulose-1,5 bisphosphate
Source: Chlamydomonas reinhardtii. Organism_taxid: 3055. Chlamydomonas reinhardtii, synechococcus sp
Biol. unit: 60mer (from PDB file)
Resolution:
2.20Å     R-factor:   0.162     R-free:   0.193
Authors: S.Karkehabadi,R.J.Spreitzer,I.Andersson
Key ref:
S.Karkehabadi et al. (2005). Chimeric small subunits influence catalysis without causing global conformational changes in the crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase. Biochemistry, 44, 9851-9861. PubMed id: 16026157 DOI: 10.1021/bi050537v
Date:
12-Mar-04     Release date:   31-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain
Seq:
Struc:
475 a.a.
465 a.a.*
Protein chains
Pfam   ArchSchema ?
P00873  (RBS1_CHLRE) -  Ribulose bisphosphate carboxylase small chain 1, chloroplastic
Seq:
Struc:
185 a.a.
122 a.a.*
Protein chains
Pfam   ArchSchema ?
P04716  (RBS_SYNP6) -  Ribulose bisphosphate carboxylase small chain
Seq:
Struc:
111 a.a.
122 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 62 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, E, F, H, I, J, K, M, O, P, R, T, V, 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 85.00% similarity
+
CO(2)
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ 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: 10.1021/bi050537v Biochemistry 44:9851-9861 (2005)
PubMed id: 16026157  
 
 
Chimeric small subunits influence catalysis without causing global conformational changes in the crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase.
S.Karkehabadi, S.R.Peddi, M.Anwaruzzaman, T.C.Taylor, A.Cederlund, T.Genkov, I.Andersson, R.J.Spreitzer.
 
  ABSTRACT  
 
Comparison of subunit sequences and X-ray crystal structures of ribulose-1,5-bisphosphate carboxylase/oxygenase indicates that the loop between beta-strands A and B of the small subunit is one of the most variable regions of the holoenzyme. In prokaryotes and nongreen algae, the loop contains 10 residues. In land plants and green algae, the loop is comprised of approximately 22 and 28 residues, respectively. Previous studies indicated that the longer betaA-betaB loop was required for the assembly of cyanobacterial small subunits with plant large subunits in isolated chloroplasts. In the present study, chimeric small subunits were constructed by replacing the loop of the green alga Chlamydomonas reinhardtii with the sequences of Synechococcus or spinach. When these engineered genes were transformed into a Chlamydomonas mutant that lacks small-subunit genes, photosynthesis-competent colonies were recovered, indicating that loop size is not essential for holoenzyme assembly. Whereas the Synechococcus loop causes decreases in carboxylation V(max), K(m)(O(2)), and CO(2)/O(2) specificity, the spinach loop causes complementary decreases in carboxylation V(max), K(m)(O(2)), and K(m)(CO(2)) without a change in specificity. X-ray crystal structures of the engineered proteins reveal remarkable similarity between the introduced betaA-betaB loops and the respective loops in the Synechococcus and spinach enzymes. The side chains of several large-subunit residues are altered in regions previously shown by directed mutagenesis to influence CO(2)/O(2) specificity. Differences in the catalytic properties of divergent Rubisco enzymes may arise from differences in the small-subunit betaA-betaB loop. This loop may be a worthwhile target for genetic engineering aimed at improving photosynthetic CO(2) fixation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21172830 M.V.Kapralov, D.S.Kubien, I.Andersson, and D.A.Filatov (2011).
Changes in Rubisco kinetics during the evolution of C4 photosynthesis in Flaveria (Asteraceae) are associated with positive selection on genes encoding the enzyme.
  Mol Biol Evol, 28, 1491-1503.  
20192734 X.G.Zhu, S.P.Long, and D.R.Ort (2010).
Improving photosynthetic efficiency for greater yield.
  Annu Rev Plant Biol, 61, 235-261.  
19734149 T.Genkov, and R.J.Spreitzer (2009).
Highly conserved small subunit residues influence rubisco large subunit catalysis.
  J Biol Chem, 284, 30105-30112.  
18974784 B.B.Menon, Z.Dou, S.Heinhorst, J.M.Shively, and G.C.Cannon (2008).
Halothiobacillus neapolitanus carboxysomes sequester heterologous and chimeric RubisCO species.
  PLoS ONE, 3, e3570.  
18664299 S.Satagopan, and R.J.Spreitzer (2008).
Plant-like substitutions in the large-subunit carboxy terminus of Chlamydomonas Rubisco increase CO2/O2 Specificity.
  BMC Plant Biol, 8, 85.  
17080589 C.A.Raines (2006).
Transgenic approaches to manipulate the environmental responses of the C3 carbon fixation cycle.
  Plant Cell Environ, 29, 331-339.  
16282373 R.J.Spreitzer, S.R.Peddi, and S.Satagopan (2005).
Phylogenetic engineering at an interface between large and small subunits imparts land-plant kinetic properties to algal Rubisco.
  Proc Natl Acad Sci U S A, 102, 17225-17230.  
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.