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PDBsum entry 3cwo

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De novo protein PDB id
3cwo
Jmol
Contents
Protein chain
236 a.a. *
Ligands
SO4
Waters ×28
* Residue conservation analysis
PDB id:
3cwo
Name: De novo protein
Title: A beta/alpha-barrel built by the combination of fragments from different folds
Structure: Beta/alpha-barrel protein based on 1thf and 1tmy. Chain: x. Engineered: yes. Other_details: residues 1-11 and 34-103 from 1tmy, 103-253 from 1thf
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
3.10Å     R-factor:   0.224     R-free:   0.256
Authors: T.A.M.Bharat,S.Eisenbeis,K.Zeth,B.Hocker
Key ref:
T.A.Bharat et al. (2008). A beta alpha-barrel built by the combination of fragments from different folds. Proc Natl Acad Sci U S A, 105, 9942-9947. PubMed id: 18632584 DOI: 10.1073/pnas.0802202105
Date:
22-Apr-08     Release date:   08-Jul-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X0C6  (HIS6_THEMA) -  Imidazole glycerol phosphate synthase subunit HisF
Seq:
Struc:
253 a.a.
236 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 63 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     1 term  

 

 
DOI no: 10.1073/pnas.0802202105 Proc Natl Acad Sci U S A 105:9942-9947 (2008)
PubMed id: 18632584  
 
 
A beta alpha-barrel built by the combination of fragments from different folds.
T.A.Bharat, S.Eisenbeis, K.Zeth, B.Höcker.
 
  ABSTRACT  
 
Combinatorial assembly of protein domains plays an important role in the evolution of proteins. There is also evidence that protein domains have come together from stable subdomains. This concept of modular assembly could be used to construct new well folded proteins from stable protein fragments. Here, we report the construction of a chimeric protein from parts of a (betaalpha)(8)-barrel enzyme from histidine biosynthesis pathway (HisF) and a protein of the (betaalpha)(5)-flavodoxin-like fold (CheY) from Thermotoga maritima that share a high structural similarity. We expected this construct to fold into a full (betaalpha)(8)-barrel. Our results show that the chimeric protein is a stable monomer that unfolds with high cooperativity. Its three-dimensional structure, which was solved to 3.1 A resolution by x-ray crystallography, confirms a barrel-like fold in which the overall structures of the parent proteins are highly conserved. The structure further reveals a ninth strand in the barrel, which is formed by residues from the HisF C terminus and an attached tag. This strand invades between beta-strand 1 and 2 of the CheY part closing a gap in the structure that might be due to a suboptimal fit between the fragments. Thus, by a combination of parts from two different folds and a small arbitrary fragment, we created a well folded and stable protein.
 
  Selected figure(s)  
 
Figure 1.
Structural comparison of half-barrels with proteins of the flavodoxin-like fold and construction of the CheYHisF chimera. (A) Topological diagram of the half-barrels [(βα)[1–4], blue] and the flavodoxin-like (βα)[5]-fold (green) (13). The structurally superimposable parts are encircled in red. β-strands are numbered. (B) Comparison of the spatial arrangement of the main secondary structural elements in (βα)[8]-barrel and flavodoxin-like proteins (top view). α-Helices are depicted as circles, and β-strands are shown as rectangles. Colors and numbering are as in A. The extra two-stranded β-sheets in the (βα)[8]-barrel are omitted for clarity; their positions are indicated by asterisks. (C) Construction of the CheYHisF chimera. The fragments originating from CheY (residue 1–11 including β1 and 34–103 including α2-β5) are depicted in green, and the fragment originating from HisF (residue 103 to 253 including α4-β8) is depicted in blue. (D) Amino acid sequence and secondary structure of the CheYHisF construct with the attached tag (boxed). Underneath the secondary structure elements are shown as observed in the crystal structure and as predicted by the program psipred (19). The lighter the shade of color in each element the smaller is the confidence of the prediction.
Figure 4.
Comparison of the CheYHisF structure to the structures of the parent proteins. HisF (PDB entry 1THF) is shown on the left, and CheY (PDB entry 1TMY) is show on the right. The parts equivalent to CheYHisF are colored in marine blue and olive green, respectively. The remainder of the folds are in gray. The superposition of CheYHisF (colors as in Fig. 3) with the parts from HisF and CheY (colored accordingly) in the center shows remarkable structural similarities, the rms deviations are indicated at the arrows. Two close-up views are shown: the lower left shows the phosphate binding sites of HisF with PO[4] and of CheYHisF filled by SO[4], and the lower right shows how β-strand 9 of CheYHisF invades between β-strands 1 and 2 sitting at the original position of β-strand 1 of CheY.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20713410 I.Yadid, and D.S.Tawfik (2011).
Functional β-propeller lectins by tandem duplications of repetitive units.
  Protein Eng Des Sel, 24, 185-195.  
21354426 S.Setiyaputra, J.P.Mackay, and W.M.Patrick (2011).
The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold.
  J Mol Biol, 408, 291-303.
PDB code: 2kzh
20368465 I.Yadid, N.Kirshenbaum, M.Sharon, O.Dym, and D.S.Tawfik (2010).
Metamorphic proteins mediate evolutionary transitions of structure.
  Proc Natl Acad Sci U S A, 107, 7287-7292.
PDB codes: 3kif 3kih
20862721 S.Eisenbeis, and B.Höcker (2010).
Evolutionary mechanism as a template for protein engineering.
  J Pept Sci, 16, 538-544.  
19751685 D.Deb, S.Vishveshwara, and S.Vishveshwara (2009).
Understanding protein structure from a percolation perspective.
  Biophys J, 97, 1787-1794.  
19237570 J.Claren, C.Malisi, B.Höcker, and R.Sterner (2009).
Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds.
  Proc Natl Acad Sci U S A, 106, 3704-3709.
PDB code: 2w79
19482467 R.I.Sadreyev, B.H.Kim, and N.V.Grishin (2009).
Discrete-continuous duality of protein structure space.
  Curr Opin Struct Biol, 19, 321-328.  
19165724 V.A.Risso, M.E.Primo, and M.R.Ermácora (2009).
Re-engineering a beta-lactamase using prototype peptides from a library of local structural motifs.
  Protein Sci, 18, 440-449.  
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.