8G9A | pdb_00008g9a

Crystal structure of a resurrected ancestor (AncRNase) of the pancreatic-type RNases 2 and 3 sub-families

PDB DOI: https://doi.org/10.2210/pdb8G9A/pdb

Classification: HYDROLASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-21 Released: 2024-02-28
Deposition Author(s): Tran, T.T.Q., Pham, N.T.H., Calmettes, C., Doucet, N.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Fonds de Recherche du Quebec - Sante (FRQS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.205 (Depositor), 0.206 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases.

Tran, T.T.Q., Narayanan, C., Loes, A.N., Click, T.H., Pham, N.T.H., Letourneau, M., Harms, M.J., Calmettes, C., Agarwal, P.K., Doucet, N.

(2024) J Biological Chem 300: 107280-107280

PubMed: 38588810 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2024.107280
Primary Citation Related Structures:
7TY1, 8F5X, 8G9A

PubMed Abstract:
Evolutionarily conserved structural folds can give rise to diverse biological functions, yet predicting atomic-scale interactions that contribute to the emergence of novel activities within such folds remains challenging. Pancreatic-type ribonucleases illustrate this complexity, sharing a core structure that has evolved to accommodate varied functions. In this study, we used ancestral sequence reconstruction to probe evolutionary and molecular determinants that distinguish biological activities within eosinophil members of the RNase 2/3 subfamily. Our investigation unveils functional, structural, and dynamical behaviors that differentiate the evolved ancestral ribonuclease (AncRNase) from its contemporary eosinophil RNase orthologs. Leveraging the potential of ancestral reconstruction for protein engineering, we used AncRNase predictions to design a minimal 4-residue variant that transforms human RNase 2 into a chimeric enzyme endowed with the antimicrobial and cytotoxic activities of RNase 3 members. This work provides unique insights into mutational and evolutionary pathways governing structure, function, and conformational states within the eosinophil RNase subfamily, offering potential for targeted modulation of RNase-associated functions.

Organizational Affiliation

Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, Quebec, Canada.

Macromolecule Content

Total Structure Weight: 64.75 kDa
Atom Count: 4,932
Modeled Residue Count: 532
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
a resurrected ancestor (AncRNase) of the pancreatic-type RNases 2 and 3 sub-families	A, B, C, D	133	synthetic construct	Mutation(s): 0 EC: 3.1.27.5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain RA [auth D] SDF format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D]	QA [auth D], RA [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain QA [auth D] Focus chain RA [auth D] Interactions & Density Focus chain QA [auth D] Focus chain RA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	EA [auth C] FA [auth C] GA [auth C] MA [auth D] N [auth A] EA [auth C], FA [auth C], GA [auth C], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], W [auth B], X [auth B], Y [auth B], Z [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.205 (Depositor), 0.206 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.29	α = 90
b = 170.29	β = 90
c = 170.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN202204368
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN201706091
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	CREATE511956
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	251848
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	281993