PDBsum entry 2pem

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Chaperone PDB id
Protein chains
(+ 0 more) 110 a.a. *
Waters ×16
* Residue conservation analysis
PDB id:
Name: Chaperone
Title: Crystal structure of rbcx in complex with substrate
Structure: Orf134. Chain: a, b, c, d, e, f. Engineered: yes. Rbcl. Chain: r. Fragment: residues 459-465. Engineered: yes
Source: Synechococcus sp.. Organism_taxid: 32049. Strain: pcc 7002. Gene: rbcx. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: synthetic peptide with the sequence based on bisphosphate carboxylase large chain (rbcl) from synechococ
2.95Å     R-factor:   0.236     R-free:   0.264
Authors: S.Saschenbrecker,A.Bracher,K.Vasudeva Rao,B.Vasudeva Rao,F.U M.Hayer-Hartl
Key ref:
S.Saschenbrecker et al. (2007). Structure and function of RbcX, an assembly chaperone for hexadecameric Rubisco. Cell, 129, 1189-1200. PubMed id: 17574029 DOI: 10.1016/j.cell.2007.04.025
03-Apr-07     Release date:   10-Jul-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q44177  (Q44177_SYNP2) -  ORF134
134 a.a.
110 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1016/j.cell.2007.04.025 Cell 129:1189-1200 (2007)
PubMed id: 17574029  
Structure and function of RbcX, an assembly chaperone for hexadecameric Rubisco.
S.Saschenbrecker, A.Bracher, K.V.Rao, B.V.Rao, F.U.Hartl, M.Hayer-Hartl.
After folding, many proteins must assemble into oligomeric complexes to become biologically active. Here we describe the role of RbcX as an assembly chaperone of ribulose-bisphosphate carboxylase/oxygenase (Rubisco), the enzyme responsible for the fixation of atmospheric carbon dioxide. In cyanobacteria and plants, Rubisco is an approximately 520 kDa complex composed of eight large subunits (RbcL) and eight small subunits (RbcS). We found that cyanobacterial RbcX functions downstream of chaperonin-mediated RbcL folding in promoting the formation of RbcL(8) core complexes. Structural analysis revealed that the 15 kDa RbcX forms a homodimer with two cooperating RbcL-binding regions. A central cleft specifically binds the exposed C-terminal peptide of RbcL subunits, enabling a peripheral surface of RbcX to mediate RbcL(8) assembly. Due to the dynamic nature of these interactions, RbcX is readily displaced from RbcL(8) complexes by RbcS, producing the active enzyme. The strategies employed by RbcX in achieving substrate specificity and efficient product release may be generally relevant in assisted assembly reactions.
  Selected figure(s)  
Figure 4.
Figure 4. Binding of C-Terminal RbcL Peptide to RbcX
(A) A cellulose membrane containing an array of overlapping dodecamer peptides covering the sequence of Syn7002-RbcL was probed with the RbcX proteins indicated. Peptide-bound RbcX was visualized by chemiluminescent immunodetection with anti-RbcX antibody.
(B) Alignment using MultAlin (Corpet, 1988) of C-terminal amino acid sequences of RbcL from the cyanobacterial and higher plant species indicated (Swiss-Prot accession numbers in brackets). High consensus level (≥ 90%) is depicted in red and low consensus level (≥ 50%) in blue.
(C) Structure of the complex of peptide EIKFEFD bound to RbcX dimer. The peptide is shown in stick representation; RbcX is represented as a molecular surface with protomers colored white and blue, respectively. N and C termini of the peptide are indicated.
(D) Magnification of boxed area in (C) presenting a view of the refined peptide bound to RbcX. Molecular interactions between peptide and RbcX are highlighted. Dashed lines represent hydrogen bonds. Residues of the RbcX monomers participating in peptide binding are displayed in stick representation below the transparent surface of the molecule and are numbered in white and yellow, respectively. The important hydrophobic residues in the bound peptide are also labeled.
Figure 7.
Figure 7. Working Model of RbcX Function in Cyanobacterial Rubisco Assembly
RbcX functions to increase the efficiency of Rubisco assembly by acting on folded RbcL subunits subsequent to their GroEL/GroES-mediated folding. Recognition of RbcX requires the exposed C-terminal RbcL peptide (see Discussion for details and Figure S11). Note that assembly of RbcL[8]S[8] may also occur independently of RbcX for some Rubisco homologs, presumably involving similar assembly intermediates.
  The above figures are reprinted by permission from Cell Press: Cell (2007, 129, 1189-1200) copyright 2007.  
  Figures were selected by an automated process.  

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
22048315 O.Mueller-Cajar, M.Stotz, P.Wendler, F.U.Hartl, A.Bracher, and M.Hayer-Hartl (2011).
Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
  Nature, 479, 194-199.
PDB codes: 3syk 3syl 3zuh
21204250 Z.Wang, and T.Wang (2011).
Dynamic proteomic analysis reveals diurnal homeostasis of key pathways in rice leaves.
  Proteomics, 11, 225-238.  
20727772 A.Chari, and U.Fischer (2010).
Cellular strategies for the assembly of molecular machines.
  Trends Biochem Sci, 35, 676-683.  
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
20075906 R.J.Ellis (2010).
Biochemistry: Tackling unintelligent design.
  Nature, 463, 164-165.  
19843217 A.M.Hirtreiter, G.Calloni, F.Forner, B.Scheibe, M.Puype, J.Vandekerckhove, M.Mann, F.U.Hartl, and M.Hayer-Hartl (2009).
Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei.
  Mol Microbiol, 74, 1152-1168.  
19623579 C.Li, W.Wang, H.Wang, Y.Zhong, J.Di, and Y.Lin (2009).
Proteomic analysis of proteins differentially expressed in uterine lymphocytes obtained from wild-type and NOD mice.
  J Cell Biochem, 108, 447-457.  
19491934 F.U.Hartl, and M.Hayer-Hartl (2009).
Converging concepts of protein folding in vitro and in vivo.
  Nat Struct Mol Biol, 16, 574-581.  
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.  
18984161 A.Chari, M.M.Golas, M.Klingenhäger, N.Neuenkirchen, B.Sander, C.Englbrecht, A.Sickmann, H.Stark, and U.Fischer (2008).
An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs.
  Cell, 135, 497-509.  
18713001 A.R.Kusmierczyk, and M.Hochstrasser (2008).
Some assembly required: dedicated chaperones in eukaryotic proteasome biogenesis.
  Biol Chem, 389, 1143-1151.  
18242075 H.R.Saibil (2008).
Chaperone machines in action.
  Curr Opin Struct Biol, 18, 35-42.  
  18765926 M.Tarnawski, S.Krzywda, A.Szczepaniak, and M.Jaskolski (2008).
Rational 'correction' of the amino-acid sequence of RbcX protein from the thermophilic cyanobacterium Thermosynechococcus elongatus dramatically improves crystallization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 870-874.  
18626786 O.Mueller-Cajar, and S.M.Whitney (2008).
Directing the evolution of Rubisco and Rubisco activase: first impressions of a new tool for photosynthesis research.
  Photosynth Res, 98, 667-675.  
18397378 Z.Havelda, E.Várallyay, A.Válóczi, and J.Burgyán (2008).
Plant virus infection-induced persistent host gene downregulation in systemically infected leaves.
  Plant J, 55, 278-288.  
17881829 S.Tanaka, M.R.Sawaya, C.A.Kerfeld, and T.O.Yeates (2007).
Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803.
  Acta Crystallogr D Biol Crystallogr, 63, 1109-1112.
PDB code: 2py8
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.