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PDBsum entry 1rba

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protein Protein-protein interface(s) links
Lyase(carbon-carbon) PDB id
1rba
Jmol PyMol
Contents
Protein chains
419 a.a. *
443 a.a. *
Waters ×110
* Residue conservation analysis
PDB id:
1rba
Name: Lyase(carbon-carbon)
Title: Substitution of asp193 to asn at the active site of ribulose bisphosphate carboxylase results in conformational changes
Structure: Rubisco. Chain: a, b. Engineered: yes. Mutation: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.207    
Authors: G.Schneider,E.Soderlind
Key ref: E.Söderlind et al. (1992). Substitution of ASP193 to ASN at the active site of ribulose-1,5-bisphosphate carboxylase results in conformational changes. Eur J Biochem, 206, 729-735. PubMed id: 1606957
Date:
18-Nov-91     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04718  (RBL2_RHORU) -  Ribulose bisphosphate carboxylase
Seq:
Struc:
466 a.a.
419 a.a.*
Protein chain
Pfam   ArchSchema ?
P04718  (RBL2_RHORU) -  Ribulose bisphosphate carboxylase
Seq:
Struc:
466 a.a.
443 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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
+ CO(2)
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
Eur J Biochem 206:729-735 (1992)
PubMed id: 1606957  
 
 
Substitution of ASP193 to ASN at the active site of ribulose-1,5-bisphosphate carboxylase results in conformational changes.
E.Söderlind, G.Schneider, S.Gutteridge.
 
  ABSTRACT  
 
The crystal structure of a mutant of ribulose bisphosphate carboxylase/oxygenase from Rhodospirillium rubrum, where Asp193, one of the ligands of the magnesium ion at the activator site, is replaced by Asn, has been determined to a nominal resolution of 0.26 nm. The mutation of Asp to Asn induces both local and global conformation changes as follows. The side chain of Asn193 moves away from the active site and interacts with main-chain oxygen of residue 165, located in the neighbouring strand beta 1 of the alpha/beta barrel. The side chain of Lys166, which forms a salt bridge with Asp193 in the wild-type enzyme, interacts with Asn54 from the second subunit and creates a new subunit-subunit interaction. Another new subunit-subunit interaction is formed, more than 1.2 nm away from the site of the mutation. In the mutant enzyme, the side chain of Asp263 interacts with the side chain of Thr106 from the second subunit. Asp193 is not part of a subunit-subunit interface area or an allosteric regulatory site. Nevertheless, replacement of this residue by Asn results, unexpectedly, in a difference in the packing of the two subunits, which can be described as a slight rotation of one of the subunits relative to the second. The observed structural changes at the active site of the enzyme provide a molecular explanation for the differing behaviour of the Asp193----Asn mutant with respect to activation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19074801 A.I.den Hollander, T.L.McGee, C.Ziviello, S.Banfi, T.P.Dryja, F.Gonzalez-Fernandez, D.Ghosh, and E.L.Berson (2009).
A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa.
  Invest Ophthalmol Vis Sci, 50, 1864-1872.  
15893668 H.Li, M.R.Sawaya, F.R.Tabita, and D.Eisenberg (2005).
Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum.
  Structure, 13, 779-789.
PDB code: 1ykw
11435112 K.Kitano, N.Maeda, T.Fukui, H.Atomi, T.Imanaka, and K.Miki (2001).
Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.
  Structure, 9, 473-481.
PDB code: 1geh
7763977 C.H.Schein (1993).
Solubility and secretability.
  Curr Opin Biotechnol, 4, 456-461.  
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.

 

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