PDBsum entry 2bkg

De novo protein

PDB id: 2bkg

Contents

Protein chains

155 a.a. *

Waters ×330

* Residue conservation analysis

PDB id:

2bkg

Name:

De novo protein

Title:

Crystal structure of e3_19 a designed ankyrin repeat protein

Structure:

Synthetic construct ankyrin repeat protein e3_19. Chain: a, b. Engineered: yes

Source:

Synthetic construct. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.178 R-free: 0.227

Authors:

H.K.Binz,A.Kohl,A.Pluckthun,M.G.Grutter

Key ref:

H.K.Binz et al. (2006). Crystal structure of a consensus-designed ankyrin repeat protein: implications for stability. Proteins, 65, 280-284. PubMed id: 16493627 DOI: 10.1002/prot.20930

Date:

16-Feb-05 Release date: 21-Jun-06

Protein chains

No UniProt id for this chain

Struc: 155 a.a.

DOI no: 10.1002/prot.20930

Proteins 65:280-284 (2006)

PubMed id: 16493627

Crystal structure of a consensus-designed ankyrin repeat protein: implications for stability.

H.K.Binz, A.Kohl, A.Plückthun, M.G.Grütter.

ABSTRACT

Consensus-designed ankyrin repeat (AR) proteins are thermodynamically very stable. The structural analysis of the designed AR protein E3_5 revealed that this stability is due to a regular fold with highly conserved structural motifs and H-bonding networks. However, the designed AR protein E3_19 exhibits a significantly lower stability than E3_5 (9.6 vs. 14.8 kcal/mol), despite 88% sequence identity. To investigate the structural correlations of this stability difference between E3_5 and E3_19, we determined the crystal structure of E3_19 at 1.9 A resolution. E3_19 as well has a regular AR domain fold with the characteristic H-bonding patterns. All structural features of the E3_5 and E3_19 molecules appear to be virtually identical (RMSD(Calpha) approximately 0.7 A). However, clear differences are observed in the surface charge distribution of the two AR proteins. E3_19 features clusters of charged residues and more exposed hydrophobic residues than E3_5. The atomic coordinates of E3_19 have been deposited in the Protein Data Bank. PDB ID: 2BKG.

Selected figure(s)

Figure 2.
Figure 2. Structural comparison of of E3_19 and E3_5. (a) Stereoview of the superposition of E3_19 (B molecule, brown) with E3_5 (PDB ID: 1MJ0, blue) in ribbon representations. The N-and C-termini are labeled for orientation. The two proteins are practically identical, with the biggest differences being observed in the C-terminal AR, where E3_5 appears to be more compact than E3_19. The two E3_19 molecules of the asymmetric unit are virtually identical (b) H-bonding in the C-terminal AR of E3_19. Asn156 makes H-bonds to Asp122 (residues in stick mode in blue). (c) H-bonding in the C-terminal AR of E3_5. Asn158 makes H-bonds to Lys122 and Ala121 (residues in stick mode in magenta).

Figure 3.
Figure 3. Charge distribution in E3_19 and E3_5. E3_19 is depicted on the left, E3_5 is depicted on the right. (a) Negative charges in the -turn regions. Negatively charged residues are depicted in stick mode in red on the backbones in ribbons. For completeness, Asp122 of E3_19 is also shown. (b) Positively charged residues (stick mode in blue) in the first three repeats of E3_19 and the first and fourth repeat of E3_5, respectively, are depicted on the backbones in ribbons. (c) Surface representations of the electrostatic potential of E3_19 and E3_5 (red = -0.5, white = 0, blue = +0.5). For orientation identically positioned ribbon representations are depicted on the left of each surface representation.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 280-284) copyright 2006.

Figures were selected by the author.