PDBsum entry 2hyz

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protein metals links
De novo protein PDB id
Protein chain
136 a.a. *
_SM ×3
Waters ×25
* Residue conservation analysis
PDB id:
Name: De novo protein
Title: Crystal structure of an 8 repeat consensus tpr superhelix (orthorombic crystal form)
Structure: Synthetic consensus tpr protein. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: the sequence of the protein was designed and then expressed in e.Coli bl21(de3), plasmid ppro-xhta
2.30Å     R-factor:   0.217     R-free:   0.270
Authors: T.Kajander,A.L.Cortajarena,L.Regan
Key ref:
T.Kajander et al. (2007). Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins. Acta Crystallogr D Biol Crystallogr, 63, 800-811. PubMed id: 17582171 DOI: 10.1107/S0907444907024353
08-Aug-06     Release date:   19-Feb-08    
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Protein chain
No UniProt id for this chain
Struc: 136 a.a.
Key:    Secondary structure  CATH domain


DOI no: 10.1107/S0907444907024353 Acta Crystallogr D Biol Crystallogr 63:800-811 (2007)
PubMed id: 17582171  
Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins.
T.Kajander, A.L.Cortajarena, S.Mochrie, L.Regan.
The structure and stability of repeat proteins has been little studied in comparison to the properties of the more familiar globular proteins. Here, the structure and stability of designed tetratricopeptide-repeat (TPR) proteins is described. The TPR is a 34-amino-acid motif which adopts a helix-turn-helix structure and occurs as tandem repeats. The design of a consensus TPR motif (CTPR) has previously been described. Here, the crystal structures and stabilities of proteins that contain eight or 20 identical tandem repeats of the CTPR motif (CTPR8 and CTPR20) are presented. Both CTPR8 and CTPR20 adopt a superhelical overall structure. The structures of the different-length CTPR proteins are compared with each other and with the structures of natural TPR domains. Also, the unusual and perhaps unique crystal-packing interactions resulting in pseudo-infinite crystalline superhelices observed in the different crystal forms of CTPR8 and CTPR20 are discussed. Finally, it is shown that the thermodynamic behavior of CTPR8 and CTPR20 can be predicted from the behavior of other TPRs in this series using an Ising model-based analysis. The designed protein series CTPR2-CTPR20 covers the natural size repertoire of TPR domains and as such is an excellent model system for natural TPR proteins.
  Selected figure(s)  
Figure 7.
Figure 7 Schematic representation of the crystal-packing interactions between superhelical molecules. (a) As an example, in P4[1]2[1]2 there are two repeats (numbered 1-8) within the asymmetric unit (indicated as AU; red box). For this arrangement there are eight equally possible two-repeat arrangements for the asymmetric unit. (b) Schematic illustration of the stacking of helices between repeats of individual molecules. The first A-helix of the next molecule must always pack against the last repeat of the previous molecule and therefore the C-terminal capping helix must be displaced. (c) Ribbon representation of the superhelical stacking with each single repeat coloured yellow or blue.
Figure 8.
Figure 8 Alignment of repeats 3-10 of the TPR domain of OGT (red) with the tetragonal crystal structure of CTPR8 (blue).
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 800-811) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20089039 A.L.Cortajarena, J.Wang, and L.Regan (2010).
Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand.
  FEBS J, 277, 1058-1066.
PDB code: 3kd7
20535822 A.Sircar, S.Chaudhury, K.P.Kilambi, M.Berrondo, and J.J.Gray (2010).
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.
  Proteins, 78, 3115-3123.  
20718048 Vries, A.S.Melquiond, P.L.Kastritis, E.Karaca, A.Bordogna, M.van Dijk, J.P.Rodrigues, and A.M.Bonvin (2010).
Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.
  Proteins, 78, 3242-3249.  
20924356 Z.Zhang, K.Kulkarni, S.J.Hanrahan, A.J.Thompson, and D.Barford (2010).
The APC/C subunit Cdc16/Cut9 is a contiguous tetratricopeptide repeat superhelix with a homo-dimer interface similar to Cdc27.
  EMBO J, 29, 3733-3744.
PDB code: 2xpi
19289204 T.Aksel, and D.Barrick (2009).
Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models.
  Methods Enzymol, 455, 95.  
19436472 A.Mor, G.Haran, and Y.Levy (2008).
Characterization of the unfolded state of repeat proteins.
  HFSP J, 2, 405-415.  
18776008 J.Koo, S.Tammam, S.Y.Ku, L.M.Sampaleanu, L.L.Burrows, and P.L.Howell (2008).
PilF is an outer membrane lipoprotein required for multimerization and localization of the Pseudomonas aeruginosa Type IV pilus secretin.
  J Bacteriol, 190, 6961-6969.
PDB code: 2ho1
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.