3ESD

cut-2b; NCN-Pt-Pincer-Cutinase Hybrid

Summary for 3ESD

• Entry DOI: 10.2210/pdb3esd/pdb
• Descriptor: Cutinase 1, bromo(4-{3-[(R)-ethoxy(4-nitrophenoxy)phosphoryl]propyl}-2,6-bis[(methylsulfanyl-kappaS)methyl]phenyl-kappaC~1~)palladium(2+) (3 entities in total)
• Functional Keywords: protein-metallopincer complex, glycoprotein, hydrolase, secreted, serine esterase
• Biological source: Fusarium solani f. pisi
• Cellular location: Secreted: P00590
• Total number of polymer chains: 1
• Total formula weight: 22948.90

Authors

Rutten, L.,Mannie, J.P.B.A.,Lutz, M.,Gros, P. (deposition date: 2008-10-05, release date: 2009-07-28, Last modification date: 2024-10-09)

Primary citation

Rutten, L.,Wieczorek, B.,Mannie, J.P.B.A.,Kruithof, C.A.,Dijkstra, H.P.,Egmond, M.R.,Lutz, M.,Klein Gebbink, R.J.M.,Gros, P.,van Koten, G.
Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids
Chemistry, 15:4270-4280, 2009

PubMed Abstract: The first crystal structures of lipases that have been covalently modified through site-selective inhibition by different organometallic phosphonate-pincer-metal complexes are described. Two ECE-pincer-type d(8)-metal complexes, that is, platinum (1) or palladium (2) with phosphonate esters (ECE = [(EtO)-(O=)P(-O-C(6)H(4)-(NO(2))-4)(-C(3)H(6)-4-(C(6)H(2)-(CH(2)E)(2))](-); E = NMe(2) or SMe) were introduced prior to crystallization and have been shown to bind selectively to the Ser(120) residue in the active site of the lipase cutinase to give cut-1 (platinum) or cut-2 (palladium) hybrids. For all five presented crystal structures, the ECE-pincer-platinum or -palladium head group sticks out of the cutinase molecule and is exposed to the solvent. Depending on the nature of the ECE-pincer-metal head group, the ECE-pincer-platinum and -palladium guests occupy different pockets in the active site of cutinase, with concomitant different stereochemistries on the phosphorous atom for the cut-1 (S(P)) and cut-2 (R(P)) structures. When cut-1 was crystallized under halide-poor conditions, a novel metal-induced dimeric structure was formed between two cutinase-bound pincer-platinum head groups, which are interconnected through a single mu-Cl bridge. This halide-bridged metal dimer shows that coordination chemistry is possible with protein-modified pincer-metal complexes. Furthermore, we could use NCN-pincer-platinum complex 1 as site-selective tool for the phasing of raw protein diffraction data, which shows the potential use of pincer-platinum complex 1 as a heavy-atom derivative in protein crystallography.

PubMed: 19219875
DOI: 10.1002/chem.200801995

Experimental method

X-RAY DIFFRACTION (1.22 Å)