1XM5

Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054

Summary for 1XM5

• Entry DOI: 10.2210/pdb1xm5/pdb
• Descriptor: Hypothetical UPF0054 protein ybeY, NICKEL (II) ION (2 entities in total)
• Functional Keywords: structural genomics, protein structure initiative, nysgxrc target t842, pfam family upf0054, psi, new york sgx research center for structural genomics, unknown function
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 70393.11

Authors

Fedorov, A.A.,Fedorov, E.V.,Shi, W.,Ramagopal, U.A.,Thirumuruhan, R.,Almo, S.C.,Burley, S.K.,New York SGX Research Center for Structural Genomics (NYSGXRC) (deposition date: 2004-10-01, release date: 2004-10-12, Last modification date: 2024-02-14)

Primary citation

Zhan, C.,Fedorov, E.V.,Shi, W.,Ramagopal, U.A.,Thirumuruhan, R.,Manjasetty, B.A.,Almo, S.C.,Fiser, A.,Chance, M.R.,Fedorov, A.A.
The ybeY protein from Escherichia coli is a metalloprotein.
Acta Crystallogr.,Sect.F, 61:959-963, 2005

PubMed Abstract: The three-dimensional crystallographic structure of the ybeY protein from Escherichia coli (SwissProt entry P77385) is reported at 2.7 A resolution. YbeY is a hypothetical protein that belongs to the UPF0054 family. The structure reveals that the protein binds a metal ion in a tetrahedral geometry. Three coordination sites are provided by histidine residues, while the fourth might be a water molecule that is not seen in the diffraction map because of its relatively low resolution. X-ray fluorescence analysis of the purified protein suggests that the metal is a nickel ion. The structure of ybeY and its sequence similarity to a number of predicted metal-dependent hydrolases provides a functional assignment for this protein family. The figures and tables of this paper were prepared using semi-automated tools, termed the Autopublish server, developed by the New York Structural GenomiX Research Consortium, with the goal of facilitating the rapid publication of crystallographic structures that emanate from worldwide Structural Genomics efforts, including the NIH-funded Protein Structure Initiative.

PubMed: 16511207
DOI: 10.1107/S1744309105031131

Experimental method

X-RAY DIFFRACTION (2.7 Å)