Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily.


Abstract

The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 x 10(2) M(-1). We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355-Glu401), as the formation of an extra alpha-helix was predicted. An NMR structural determination confirmed the formation of an alpha-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal alpha-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain. Study holds ProTherm entries: 24896, 24897, 24898, 24899, 24900, 24901, 24902, 24903 Extra Details: Region 355-390 WW domain; dimerization; stability; dynamics; ultracentrifuge; NMR

Submission Details

ID: TzxedoMZ3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:55 p.m.

Version: 1

Publication Details
Ohnishi S;Tochio N;Tomizawa T;Akasaka R;Harada T;Seki E;Sato M;Watanabe S;Fujikura Y;Koshiba S;Terada T;Shirouzu M;Tanaka A;Kigawa T;Yokoyama S,Protein Sci. (2008) Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily. PMID:18562638
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
2KPK 2010-10-27 MAGI-1 PDZ1
2YSE 2007-10-09 Solution structure of the second WW domain from the human membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1. MAGI-1
2KPL 2010-10-27 MAGI-1 PDZ1 / E6CT
2YSD 2007-10-09 Solution structure of the first WW domain from the human membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1. MAGI-1
2ZAJ 2008-04-15 Solution structure of the short-isoform of the second WW domain from the human membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 (MAGI-1)
3BPU 2008-01-08 1.6 Crystal structure of the 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant
5ZYS 2019-01-23 1.78 Structure of Nephrin/MAGI1 complex
2Q9V 2007-06-26 2.0 Crystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase
2R4H 2007-10-16 2.05 Crystal structure of a C1190S mutant of the 6th PDZ domain of human membrane associated guanylate kinase
2I04 2007-02-20 2.15 X-ray crystal structure of MAGI-1 PDZ1 bound to the C-terminal peptide of HPV18 E6
5N7D 2017-11-08 2.3 MAGI-1 complexed with a RSK1 peptide
5N7F 2017-11-08 2.3 MAGI-1 complexed with a pRSK1 peptide
1WBP 2005-10-19 2.4 SRPK1 bound to 9mer docking motif peptide
5N7G 2017-11-08 2.95 MAGI-1 complexed with a synthetic pRSK1 peptide

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
97.2 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 Q4L1J4 MAGI1_RAT
97.2 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 Q6RHR9 MAGI1_MOUSE
100.0 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 Q96QZ7 MAGI1_HUMAN