1T6W

RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES

Summary for 1T6W

• Entry DOI: 10.2210/pdb1t6w/pdb
• NMR Information: BMRB: 6201
• Descriptor: hypothetical protein XP_346638, CALCIUM ION (2 entities in total)
• Functional Keywords: calcium-binding protein, cd2, design, metal binding protein
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Membrane; Single-pass type I membrane protein: P08921
• Total number of polymer chains: 1
• Total formula weight: 11199.70

Authors

Yang, W.,Wilkins, A.L.,Ye, Y.,Liu, Z.-R.,Urbauer, J.L.,Kearney, A.,van der Merwe, P.A.,Yang, J.J. (deposition date: 2004-05-07, release date: 2005-02-15, Last modification date: 2024-05-22)

Primary citation

Yang, W.,Wilkins, A.L.,Ye, Y.,Liu, Z.R.,Li, S.Y.,Urbauer, J.L.,Hellinga, H.W.,Kearney, A.,van der Merwe, P.A.,Yang, J.J.
Design of a calcium-binding protein with desired structure in a cell adhesion molecule.
J.Am.Chem.Soc., 127:2085-2093, 2005

PubMed Abstract: Ca2+, "a signal of life and death", controls numerous cellular processes through interactions with proteins. An effective approach to understanding the role of Ca2+ is the design of a Ca2+-binding protein with predicted structural and functional properties. To design de novo Ca2+-binding sites in proteins is challenging due to the high coordination numbers and the incorporation of charged ligand residues, in addition to Ca2+-induced conformational change. Here, we demonstrate the successful design of a Ca2+-binding site in the non-Ca2+-binding cell adhesion protein CD2. This designed protein, Ca.CD2, exhibits selectivity for Ca2+ versus other di- and monovalent cations. In addition, La3+ (Kd 5.0 microM) and Tb3+ (Kd 6.6 microM) bind to the designed protein somewhat more tightly than does Ca2+ (Kd 1.4 mM). More interestingly, Ca.CD2 retains the native ability to associate with the natural target molecule. The solution structure reveals that Ca.CD2 binds Ca2+ at the intended site with the designed arrangement, which validates our general strategy for designing de novo Ca2+-binding proteins. The structural information also provides a close view of structural determinants that are necessary for a functional protein to accommodate the metal-binding site. This first success in designing Ca2+-binding proteins with desired structural and functional properties opens a new avenue in unveiling key determinants to Ca2+ binding, the mechanism of Ca2+ signaling, and Ca2+-dependent cell adhesion, while avoiding the complexities of the global conformational changes and cooperativity in natural Ca2+-binding proteins. It also represents a major achievement toward designing functional proteins controlled by Ca2+ binding.

PubMed: 15713084
DOI: 10.1021/ja0431307

Experimental method

SOLUTION NMR