Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families.
We present a detailed comparative analysis of the PDZ domains of the human LAP proteins Erbin, Densin-180, and Scribble and the MAGUK ZO-1. Phage-displayed peptide libraries and in vitro affinity assays were used to define ligand binding profiles for each domain. The analysis reveals the importance of interactions with all four C-terminal residues of the ligand, which constitute a core recognition motif, and also the role of interactions with more upstream ligand residues that support and modulate the core binding interaction. In particular, the results highlight the importance of site(-1), which interacts with the penultimate residue of ligand C termini. Site(-1) was found to be monospecific in the Erbin PDZ domain (accepts tryptophan only), bispecific in the first PDZ domain of ZO-1 (accepts tryptophan or tyrosine), and promiscuous in the Scribble PDZ domains. Furthermore, it appears that the level of promiscuity within site(-1) greatly influences the range of potential biological partners and functions that can be associated with each protein. These findings show that subtle changes in binding specificity can significantly alter the range of biological partners for PDZ domains, and the insights enhance our understanding of this diverse family of peptide-binding modules.
Zhang
Yingnan
Y
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.
Yeh
Sherry
S
Department of Assay Automation, Genentech, Inc., South San Francisco, California 94080.
Appleton
Brent A
BA
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.
Held
Heike A
HA
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.
Kausalya
P Jaya
PJ
Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Republic of Singapore.
Phua
Dominic C Y
DCY
Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Republic of Singapore.
Lee Wong
Wai
W
Department of Assay Automation, Genentech, Inc., South San Francisco, California 94080.
Lasky
Laurence A
LA
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.
Wiesmann
Christian
C
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.
Hunziker
Walter
W
Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Republic of Singapore.
Sidhu
Sachdev S
SS
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080. Electronic address: sidhu@gene.com.
D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry / Q000378:metabolism; D020816:Amino Acid Motifs; D001665:Binding Sites; D006801:Humans; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D019151:Peptide Library; D010455:Peptides / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D012795:Sialoglycoproteins / Q000737:chemistry / Q000378:metabolism; D025521:Tumor Suppressor Proteins / Q000737:chemistry / Q000378:metabolism; D062826:Zonula Occludens-1 Protein
D048868:Adaptor Proteins, Signal Transducing; C413364:ERBIN protein, human; C504461:LRRC7 protein, human; D008024:Ligands; D008565:Membrane Proteins; D019151:Peptide Library; D010455:Peptides; D010750:Phosphoproteins; C480591:SCRIB protein, human; D012795:Sialoglycoproteins; C569042:TJP1 protein, human; D025521:Tumor Suppressor Proteins; D062826:Zonula Occludens-1 Protein