4C6Y

Ancestral PNCA (last common ancestors of Gram-positive and Gram- negative bacteria) beta-lactamase class A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.799 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Phenotypic Comparisons of Consensus Variants Versus Laboratory Resurrections of Precambrian Proteins.

Risso, V.A.Gavira, J.A.Gaucher, E.A.Sanchez-Ruiz, J.M.

(2014) Proteins 82: 887

  • DOI: 10.1002/prot.24575
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 pre ...

    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.


    Related Citations: 
    • Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian Beta-Lactamases.
      Risso, V.A.,Gavira, J.A.,Mejia-Carmona, D.F.,Gaucher, E.A.,Sanchez-Ruiz, J.M.
      (2013) J.Am.Chem.Soc. 135: 2899


    Organizational Affiliation

    Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, 18071, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE
A, B
262N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.799 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.581α = 90.00
b = 57.473β = 90.00
c = 240.401γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection