skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family

Abstract

Protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP-ECOLI; NESG target ID: ER111; Wunderlich et al., 2004) is a 113-residue member of the UPF0131 protein family (Pfam ID: PF03674) of unknown function. This domain family is found in organisms from all three kingdoms, archaea, eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 97% of backbone and 91% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a mixed a/b topology,????????. BMRB deposit with Accession No. 6448. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
876995
Report Number(s):
PNWD-SA-7240
10492; 11701; 1887; 10492a; 2450; 7598; 3992; 3339; 2610; 2327; 2170; TRN: US200608%%358
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Biomolecular NMR; Journal Volume: 33; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CHEMICAL SHIFT; ESCHERICHIA COLI; PROTEINS; RESONANCE; SCALARS; TARGETS; TOPOLOGY; Environmental Molecular Sciences Laboratory

Citation Formats

Aramini, James M., Swapna, G.V.T., Huang, Yuanpeng, Rajan, Paranji K., Xiao, Rong, Shastry, Ritu, Acton, Thomas, Cort, John R., Kennedy, Michael A., and Montelione, Gaetano. 1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family. United States: N. p., 2005. Web. doi:10.1007/s10858-005-2597-z.
Aramini, James M., Swapna, G.V.T., Huang, Yuanpeng, Rajan, Paranji K., Xiao, Rong, Shastry, Ritu, Acton, Thomas, Cort, John R., Kennedy, Michael A., & Montelione, Gaetano. 1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family. United States. doi:10.1007/s10858-005-2597-z.
Aramini, James M., Swapna, G.V.T., Huang, Yuanpeng, Rajan, Paranji K., Xiao, Rong, Shastry, Ritu, Acton, Thomas, Cort, John R., Kennedy, Michael A., and Montelione, Gaetano. Tue . "1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family". United States. doi:10.1007/s10858-005-2597-z.
@article{osti_876995,
title = {1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family},
author = {Aramini, James M. and Swapna, G.V.T. and Huang, Yuanpeng and Rajan, Paranji K. and Xiao, Rong and Shastry, Ritu and Acton, Thomas and Cort, John R. and Kennedy, Michael A. and Montelione, Gaetano},
abstractNote = {Protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP-ECOLI; NESG target ID: ER111; Wunderlich et al., 2004) is a 113-residue member of the UPF0131 protein family (Pfam ID: PF03674) of unknown function. This domain family is found in organisms from all three kingdoms, archaea, eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 97% of backbone and 91% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a mixed a/b topology,????????. BMRB deposit with Accession No. 6448. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.},
doi = {10.1007/s10858-005-2597-z},
journal = {Journal of Biomolecular NMR},
number = 3,
volume = 33,
place = {United States},
year = {Tue Nov 01 00:00:00 EST 2005},
month = {Tue Nov 01 00:00:00 EST 2005}
}
  • The recently sequenced genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 (contig 83.1_1_243_746) contains the sequence for an hypothetical protein that falls into the DUF683 family. As observed for the other 54 DUF683 proteins currently listed in the GenBank database, this 78-residue (9.0 kDa) protein in Cyanothece is also found in a nitrogen fixation gene cluster suggesting that it is involved in the process. To date no structural information exists for any of the proteins in the DUF683 family. In an effort to elucidate the biochemical role DUF683 may play in nitrogen fixation and to obtain structural information formore » a member of the DUF683 protein family, a construct containing DUF683 from Cyanothece 51142 was generated, expressed, purified, and the solution properties characterized. A total rotational correlation time (tc) of 17.1 ns was estimated by nuclear magnetic resonance (NMR) spectroscopy suggesting a molecular weight of ~ 40 kDa, an observation dictating that DUF683 is a tetramer in solution. Using triple-labeled (2H, 13C, 15N) and residue-specific 15N-labeled amino acids (L, K, V, and E/Q) samples, most of the backbone and side chain resonances for DUF683 were assigned. The 13C alpha chemical shifts and NOESY NMR data indicate that the protein is helical from K18-E75.« less
  • 1H, 13C and 15N resonance assignments and secondary structure of the c-Myc binding domain (MBD) and the SH3 domain of the tumor suppressor Bin1
  • The product of gene locus BB0938 from Bordetella bronchiseptica (Swiss-Prot ID: Q7WNU7-BORBR; NESG target ID: BoR11; Wunderlich et al., 2004; Pfam ID: PF03476) is a 128-residue protein of unknown function. This broadly conserved protein family is found in eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 98% of backbone and 94% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a b topology with a seven-residue helical insert, ??????????. BMRB deposit with accession number 6693. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.
  • Protein design represents one of the great challenges of computational structural biology. The ability to successfully design new proteins would allow us to generate new reagents and enzymes, while at the same time providing us with an understanding of the principles of protein stability. Here we report 1H, 15N and 13C resonance assignments of a redesigned U1A protein, URNdesign. U1A has been studied extensively by our group and hence was chosen as a design target. For the assignments we sued 2D and 3D heteronuclearNMR experiments with uniformly 13C, 15N-labeled URNdesign. The assignments for the backbone NH, CO,Ca and Cb nucleimore » are 94%complete. Sidechain 1Hand13C, aromatic andQ/NNH2 resonances are essentially complete with guanidinium and K NH3 residues unassigned. BMRB deposit with accession number 6493« less