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PDBsum entry 3rub

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protein ligands Protein-protein interface(s) links
Lyase(carbon-carbon) PDB id
3rub
Jmol
Contents
Protein chains
441 a.a. *
123 a.a. *
Ligands
SO4 ×3
ASN
Waters ×216
* Residue conservation analysis
PDB id:
3rub
Name: Lyase(carbon-carbon)
Title: Crystal structure of the unactivated form of ribulose-1,5-bi carboxylase(slash)oxygenase from tobacco refined at 2.0-ang resolution
Structure: Ribulose 1,5-bisphosphate carboxylase/oxygenase, chain: l. Engineered: yes. Ribulose 1,5-bisphosphate carboxylase/oxygenase, chain: s. Engineered: yes
Source: Nicotiana tabacum. Tobacco. Organism_taxid: 4097.
Biol. unit: 60mer (from PQS)
Resolution:
2.00Å     R-factor:   0.171    
Authors: H.Schreuder,D.Cascio,P.M.G.Curmi,M.S.Chapman,S.W.Suh,D.S.Eis
Key ref: P.M.Curmi et al. (1992). Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution. J Biol Chem, 267, 16980-16989. PubMed id: 1512238
Date:
25-May-90     Release date:   15-Oct-92    
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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
+ 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    
 
 
J Biol Chem 267:16980-16989 (1992)
PubMed id: 1512238  
 
 
Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution.
P.M.Curmi, D.Cascio, R.M.Sweet, D.Eisenberg, H.Schreuder.
 
  ABSTRACT  
 
The structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase was refined at a resolution of 2.0 A to an R-factor of 17.1%. The previous model (Chapman et al., 1988) was extensively rebuilt, and the small subunit was retraced. The refined model consists of residues 22-63 and 69-467 of the large subunit and the complete small subunit. A striking feature of the model is that several loops have very high B-factors, probably representing mobile regions of the molecule. An examination of the intersubunit contacts shows that the L8S8 hexadecamer is composed of four L2 dimers. The dominant contacts between these L2 dimers are formed by the small subunits. This suggests that the small subunits may be essential for maintaining the integrity of the L8S8 structure. The active site shows differences between the unactivated form and the quaternary complex. In particular, Lys334 has moved out of the active site by about 10A. This residue lies on loop 6 of the alpha beta barrel, which is a particularly mobile loop. The site of ribulose-1,5-bisphosphate carboxylase/oxygenase activation is well ordered in the absence of the carbamylation of Lys201 and Mg2+ binding. The residues are held poised by a network of hydrogen bonds. In the unactivated state, the active site is accessible to substrate binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21765418 A.Bracher, A.Starling-Windhof, F.U.Hartl, and M.Hayer-Hartl (2011).
Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco.
  Nat Struct Mol Biol, 18, 875-880.
PDB code: 3rg6
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
17574029 S.Saschenbrecker, A.Bracher, K.V.Rao, B.V.Rao, F.U.Hartl, and M.Hayer-Hartl (2007).
Structure and function of RbcX, an assembly chaperone for hexadecameric Rubisco.
  Cell, 129, 1189-1200.
PDB codes: 2pei 2pej 2pek 2pem 2pen 2peo 2peq
17163439 C.Marchand, P.Le Maréchal, Y.Meyer, and P.Decottignies (2006).
Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin.
  Proteomics, 6, 6528-6537.  
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
11439139 S.M.Whitney, P.Baldet, G.S.Hudson, and T.J.Andrews (2001).
Form I Rubiscos from non-green algae are expressed abundantly but not assembled in tobacco chloroplasts.
  Plant J, 26, 535-547.  
8805582 G.J.Kleywegt, and A.T.Brünger (1996).
Checking your imagination: applications of the free R value.
  Structure, 4, 897-904.  
8548461 T.C.Taylor, and I.Andersson (1996).
Structural transitions during activation and ligand binding in hexadecameric Rubisco inferred from the crystal structure of the activated unliganded spinach enzyme.
  Nat Struct Biol, 3, 95.  
8548451 T.J.Andrews (1996).
The bait in the Rubisco mousetrap.
  Nat Struct Biol, 3, 3-7.  
7922027 J.Newman, and S.Gutteridge (1994).
Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate.
  Structure, 2, 495-502.
PDB code: 1rsc
  8142899 K.Y.Zhang, D.Cascio, and D.Eisenberg (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.
PDB code: 1rlc
  8045252 M.Delarue, A.Poterszman, S.Nikonov, M.Garber, D.Moras, and J.C.Thierry (1994).
Crystal structure of a prokaryotic aspartyl tRNA-synthetase.
  EMBO J, 13, 3219-3229.  
8159715 M.J.Bennett, S.Choe, and D.Eisenberg (1994).
Domain swapping: entangling alliances between proteins.
  Proc Natl Acad Sci U S A, 91, 3127-3131.  
7846026 V.N.Maiorov, and G.M.Crippen (1994).
Learning about protein folding via potential functions.
  Proteins, 20, 167-173.  
8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
  8401235 C.Colovos, and T.O.Yeates (1993).
Verification of protein structures: patterns of nonbonded atomic interactions.
  Protein Sci, 2, 1511-1519.  
  8358297 G.J.Lee, K.A.McDonald, and B.A.McFadden (1993).
Leucine 332 influences the CO2/O2 specificity factor of ribulose-1,5-bisphosphate carboxylase/oxygenase from Anacystis nidulans.
  Protein Sci, 2, 1147-1154.  
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.  
  8358296 H.A.Schreuder, S.Knight, P.M.Curmi, I.Andersson, D.Cascio, R.M.Sweet, C.I.Brändén, and D.Eisenberg (1993).
Crystal structure of activated tobacco rubisco complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate.
  Protein Sci, 2, 1136-1146.  
8433995 M.Wilmanns, and D.Eisenberg (1993).
Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.
  Proc Natl Acad Sci U S A, 90, 1379-1383.  
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.