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PDBsum entry 5rub

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protein Protein-protein interface(s) links
Lyase(carbon-carbon) PDB id
5rub
Jmol
Contents
Protein chains
436 a.a. *
Waters ×736
* Residue conservation analysis
PDB id:
5rub
Name: Lyase(carbon-carbon)
Title: Crystallographic refinement and structure of ribulose-1,5- bisphosphate carboxylase from rhodospirillum rubrum at 1.7 angstroms resolution
Structure: Rubisco (ribulose-1,5-bisphosphate carboxylase(slash)oxygenase). Chain: a, b. Engineered: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.180    
Authors: G.Schneider,Y.Lindqvist,T.Lundqvist
Key ref: G.Schneider et al. (1990). Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution. J Mol Biol, 211, 989. PubMed id: 2107319 DOI: 10.1016/0022-2836(90)90088-4
Date:
29-May-90     Release date:   15-Oct-91    
Supersedes: 2rub
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04718  (RBL2_RHORU) -  Ribulose bisphosphate carboxylase
Seq:
Struc:
466 a.a.
436 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: 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    
 
 
DOI no: 10.1016/0022-2836(90)90088-4 J Mol Biol 211:989 (1990)
PubMed id: 2107319  
 
 
Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution.
G.Schneider, Y.Lindqvist, T.Lundqvist.
 
  ABSTRACT  
 
The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-restrained least-squares refinement program of Sussman and the restrained least-squares refinement program of Hendrickson & Konnert. The crystallographic refinement, based on 76,452 reflections with F greater than sigma (F) in the resolution range 5.5 to 1.7 A resulted in a crystallographic R-factor of 18.0%. The asymmetric unit contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The geometry of the refined model is close to ideal, with root-mean-square deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two loop regions, comprising residues 54 to 63 and 324 to 335, and the last ten amino acid residues at the C terminus are disordered in our crystals. The expected trimodal distribution is obtained for the side-chain chi 1-angles with a marked preference for staggered conformation. The hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel sheet in the beta/alpha-barrel is described. A number of hydrogen bonds and salt bridges are involved in domain-domain and subunit-subunit interactions. The subunit-subunit interface in the dimer covers an area of 2800 A2. Considerable deviations from the local 2-fold symmetry are found at both the N terminus (residues 2 to 5) and the C terminus (residues 422 to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a different conformation in the two subunits. A number of amino acid side-chains have different conformations in the two subunits. Most of these residues are located at the surface of the protein. An analysis of the individual temperature factors indicates a high mobility of the C-terminal region and for some of the loops at the active site. The positions and B-factors for 736 solvent sites have been refined (average B: 45.9 A2). Most of the solvent molecules are bound as clusters to the protein. The active site of the enzyme, especially the environment of the activator Lys191 in the non-activated enzyme is described. Crystallographic refinement at 1.7 A resolution clearly revealed the presence of a cis-proline at the active site. This residue is part of the highly conserved region Lys166-Pro167-Lys168.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20075914 C.Liu, A.L.Young, A.Starling-Windhof, A.Bracher, S.Saschenbrecker, B.V.Rao, K.V.Rao, O.Berninghausen, T.Mielke, F.U.Hartl, R.Beckmann, and M.Hayer-Hartl (2010).
Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
  Nature, 463, 197-202.
PDB codes: 2wvw 3hyb
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
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
15469819 Z.Lin, and H.S.Rye (2004).
Expansion and compression of a protein folding intermediate by GroEL.
  Mol Cell, 16, 23-34.  
12070156 N.Maeda, T.Kanai, H.Atomi, and T.Imanaka (2002).
The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability.
  J Biol Chem, 277, 31656-31662.  
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
10221918 M.Shtilerman, G.H.Lorimer, and S.W.Englander (1999).
Chaperonin function: folding by forced unfolding.
  Science, 284, 822-825.  
10089435 S.Hansen, E.Hough, and K.Andersen (1999).
Purification, crystallization and preliminary X-ray studies of two isoforms of Rubisco from Alcaligenes eutrophus.
  Acta Crystallogr D Biol Crystallogr, 55, 310-313.  
  9385633 A.C.Wallace, N.Borkakoti, and J.M.Thornton (1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
  Protein Sci, 6, 2308-2323.  
  8550452 J.M.Hernandez, S.H.Baker, S.C.Lorbach, J.M.Shively, and F.R.Tabita (1996).
Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.
  J Bacteriol, 178, 347-356.  
  8762144 S.Janecek (1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
  Protein Sci, 5, 1136-1143.  
  7549888 S.Janecek (1995).
Similarity of different beta-strands flanked in loops by glycines and prolines from distinct (alpha/beta)8-barrel enzymes: chance or a homology?
  Protein Sci, 4, 1239-1242.  
8592705 T.Sandalova, and Y.Lindqvist (1995).
Three-dimensional model of the alpha-subunit of bacterial luciferase.
  Proteins, 23, 241-255.  
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
8041699 M.T.Clegg, B.S.Gaut, G.H.Learn, and B.R.Morton (1994).
Rates and patterns of chloroplast DNA evolution.
  Proc Natl Acad Sci U S A, 91, 6795-6801.  
8234342 H.A.Schreuder, S.Knight, P.M.Curmi, I.Andersson, D.Cascio, C.I.Brändén, and D.Eisenberg (1993).
Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form.
  Proc Natl Acad Sci U S A, 90, 9968-9972.  
8141995 S.Janecek, and S.Baláz (1993).
Evolution of parallel beta/alpha-barrel enzyme family lightened by structural data on starch-processing enzymes.
  J Protein Chem, 12, 509-514.  
1606957 E.Söderlind, G.Schneider, and S.Gutteridge (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.
PDB code: 1rba
1603801 G.G.Lu, Y.Lindqvist, and G.Schneider (1992).
Electrostatic fields at the active site of ribulose-1,5-bisphosphate carboxylase.
  Proteins, 12, 117-127.  
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 codes are shown on the right.