Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain.


Abstract

The robustness of proteins against point mutations implies that only a small subset of residues determines functional properties. We test this prediction using photoactive yellow protein (PYP), a 125-residue prototype of the PER-ARNT-SIM (PAS) domain superfamily of signaling proteins. PAS domains are defined by a small number of conserved residues of unknown function. We report high-throughput biophysical measurements on a complete Ala scan set of purified PYP mutants. The dataset of 1,193 values on active site properties, functional kinetics, stability, and production level reveals that 124 mutants retain the characteristic photocycle of PYP, but that the majority of substitutions significantly alter functional properties. Only 35% of substitutions that strongly affect function are located at the active site. Unexpectedly, most PAS-conserved residues are required for maintaining protein production. PAS domain activation often involves conformational changes in α-helices linked to the PAS core. However, the mechanism of transmission and kinetic regulation of allosteric structural changes from the PAS domain to these helices is not clear. The Ala scan data reveal interactions governing allosteric switching in PYP. The photocycle kinetics is significantly altered by substitutions at 58 positions and spans a 3,000-fold range. Nine residues that dock the N-terminal α-helices of PYP to its PAS core regulate signaling kinetics. Ile39 and Asn43 are identified as part of a mechanism for regulating allosteric switching that is conserved among PAS domains. These results show that PYP combines robustness with a high degree of evolvability and imply production level as an important factor in protein evolution.

Submission Details

ID: GdG9j3sb

Submitter: Shu-Ching Ou

Submission Date: Aug. 1, 2018, 3:27 p.m.

Version: 1

Publication Details
Philip AF;Kumauchi M;Hoff WD,Proc Natl Acad Sci U S A (2010) Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain. PMID:20889915
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1D7E 1999-10-17T00:00:00+0000 1.39 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN
1F98 2000-07-07T00:00:00+0000 1.15 CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANT T50V
1F9I 2000-07-10T00:00:00+0000 1.1 CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANT Y42F
1GSV 2002-01-08T00:00:00+0000 1.75 Crystal structure of the P65 crystal form of photoactive yellow protein G47S mutant
1GSW 2002-01-09T00:00:00+0000 1.85 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G51S MUTANT
1GSX 2002-01-09T00:00:00+0000 1.79 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G47S/G51S MUTANT
1KOU 2001-12-22T00:00:00+0000 1.16 Crystal Structure of the Photoactive Yellow Protein Reconstituted with Caffeic Acid at 1.16 A Resolution
1NWZ 2003-02-07T00:00:00+0000 0.82 PYP Ultra-high resolution structure of a Bacterial Photoreceptor
1ODV 2003-03-14T00:00:00+0000 1.14 Photoactive yellow protein 1-25 deletion mutant
1OT6 2003-03-21T00:00:00+0000 0.95 CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN UNDER CONTINUOUS ILLUMINATION AT 110K

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Photoactive yellow protein P16113 PYP_HALHA