8VLK | pdb_00008vlk

Crystal structure of the yeast cytosine deaminase containing both open and closed active sites

PDB DOI: https://doi.org/10.2210/pdb8VLK/pdb

Classification: ANTIFUNGAL PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-11 Released: 2024-08-21
Deposition Author(s): Picard, M.-E., Grenier, J., Despres, P.C., Dube, A.K., Landry, C.R., Shi, R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.194 (Depositor), 0.200 (DCC)
R-Value Work:
0.161 (Depositor), 0.172 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Compensatory mutations potentiate constructive neutral evolution by gene duplication.

Despres, P.C., Dube, A.K., Picard, M.E., Grenier, J., Shi, R., Landry, C.R.

(2024) Science 385: 770-775

PubMed: 39146405 Search on PubMed
DOI: https://doi.org/10.1126/science.ado5719
Primary Citation Related Structures:
8VLJ, 8VLK, 8VLL, 8VLM

PubMed Abstract:
The functions of proteins generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicated and evolved a homodimeric enzyme to determine whether and how this could happen. We identified hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when coexpressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.

Organizational Affiliation

Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie Université Laval, Québec, QC G1V 0A6, Canada.

Macromolecule Content

Total Structure Weight: 72.08 kDa
Atom Count: 5,222
Modeled Residue Count: 611
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B, C, D	161	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: FCY1, YPR062W, YP9499.17 EC: 3.5.4.1
UniProt
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12178 Go to UniProtKB: Q12178
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12178
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain H [auth A]	H [auth A], M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], L [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain P [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] N [auth D] E [auth A], F [auth A], I [auth B], J [auth B], N [auth D], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.194 (Depositor), 0.200 (DCC)
R-Value Work: 0.161 (Depositor), 0.172 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.865	α = 90
b = 40.825	β = 104.79
c = 97.728	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2020-06954
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)	Canada	298169