1XCR

Crystal Structure of Longer Splice Variant of PTD012 from Homo sapiens reveals a novel Zinc-containing fold

Summary for 1XCR

• Entry DOI: 10.2210/pdb1xcr/pdb
• Descriptor: hypothetical protein PTD012, ZINC ION, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: structural genomics, zinc-containing fold, splice variant, acetate buffer, metal binding protein
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: Q9H0W9
• Total number of polymer chains: 2
• Total formula weight: 70603.41

Authors

Manjasetty, B.A.,Fieber-Erdmann, M.,Roske, Y.,Goetz, F.,Buessow, K.,Heinemann, U. (deposition date: 2004-09-03, release date: 2005-09-27, Last modification date: 2024-04-03)

Primary citation

Manjasetty, B.A.,Buessow, K.,Fieber-Erdmann, M.,Roske, Y.,Gobom, J.,Scheich, C.,Goetz, F.,Niesen, F.H.,Heinemann, U.
Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold
Protein Sci., 15:914-920, 2006

PubMed Abstract: The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 A resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an alphabetabetaalpha four-layer topology. A metal ion residing between the central beta-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn(2+). Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn(2+) to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and beta-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.

PubMed: 16522806
DOI: 10.1110/ps.052037006

Experimental method

X-RAY DIFFRACTION (1.7 Å)