4C6Y image
Deposition Date 2013-09-19
Release Date 2014-04-16
Last Version Date 2023-12-20
Entry Detail
PDB ID:
4C6Y
Keywords:
Title:
Ancestral PNCA (last common ancestors of Gram-positive and Gram- negative bacteria) beta-lactamase class A
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:BETA-LACTAMASE
Chain IDs:A, B
Chain Length:262
Number of Molecules:2
Biological Source:SYNTHETIC CONSTRUCT
Primary Citation
Phenotypic Comparisons of Consensus Variants Versus Laboratory Resurrections of Precambrian Proteins.
Proteins 82 887 ? (2014)
PMID: 24710963 DOI: 10.1002/PROT.24575

Abstact

Consensus-sequence engineering has generated protein variants with enhanced stability, and sometimes, with modulated biological function. Consensus mutations are often interpreted as the introduction of ancestral amino acid residues. However, the precise relationship between consensus engineering and ancestral protein resurrection is not fully understood. Here, we report the properties of proteins encoded by consensus sequences derived from a multiple sequence alignment of extant, class A β-lactamases, as compared with the properties of ancient Precambrian β-lactamases resurrected in the laboratory. These comparisons considered primary sequence, secondary, and tertiary structure, as well as stability and catalysis against different antibiotics. Out of the three consensus variants generated, one could not be expressed and purified (likely due to misfolding and/or low stability) and only one displayed substantial stability having substrate promiscuity, although to a lower extent than ancient β-lactamases. These results: (i) highlight the phenotypic differences between consensus variants and laboratory resurrections of ancestral proteins; (ii) question interpretations of consensus proteins as phenotypic proxies of ancestral proteins; and (iii) support the notion that ancient proteins provide a robust approach toward the preparation of protein variants having large numbers of mutational changes while possessing unique biomolecular properties.

Legend

Protein

Chemical

Disease

Primary Citation of related structures