5HEB

The third PDZ domain from the synaptic protein PSD-95 in complex with a C-terminal peptide derived from CRIPT

Summary for 5HEB

• Entry DOI: 10.2210/pdb5heb/pdb
• Related: 1BE9 5HDY 5HED 5HET 5HEY 5HF1 5HF4 5HFB 5HFC 5HFD 5HFE 5HFF
• Descriptor: Disks large homolog 4, Cysteine-rich PDZ-binding protein, GLYCEROL, ... (4 entities in total)
• Functional Keywords: pdz, glgf, dhr, adhesion, synapse, synaptic density, peptide-binding domain, peptide binding protein
• Biological source: Rattus norvegicus (Rat); More
• Cellular location: Cell membrane; Peripheral membrane protein: P31016; Cytoplasm : Q792Q4
• Total number of polymer chains: 2
• Total formula weight: 13992.45

Authors

White, K.I.,Raman, A.S.,Ranganathan, R. (deposition date: 2016-01-05, release date: 2016-11-16, Last modification date: 2023-09-27)

Primary citation

Raman, A.S.,White, K.I.,Ranganathan, R.
Origins of Allostery and Evolvability in Proteins: A Case Study.
Cell(Cambridge,Mass.), 166:468-480, 2016

PubMed Abstract: Proteins display the capacity for adaptation to new functions, a property critical for evolvability. But what structural principles underlie the capacity for adaptation? Here, we show that adaptation to a physiologically distinct class of ligand specificity in a PSD95, DLG1, ZO-1 (PDZ) domain preferentially occurs through class-bridging intermediate mutations located distant from the ligand-binding site. These mutations provide a functional link between ligand classes and demonstrate the principle of "conditional neutrality" in mediating evolutionary adaptation. Structures show that class-bridging mutations work allosterically to open up conformational plasticity at the active site, permitting novel functions while retaining existing function. More generally, the class-bridging phenotype arises from mutations in an evolutionarily conserved network of coevolving amino acids in the PDZ family (the sector) that connects the active site to distant surface sites. These findings introduce the concept that allostery in proteins could have its origins not in protein function but in the capacity to adapt.

PubMed: 27321669
DOI: 10.1016/j.cell.2016.05.047

Experimental method

X-RAY DIFFRACTION (1.65 Å)