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Solution NMR structure of the helicase associated domain BVU_0683(627–691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA

  • Published:
Journal of Structural and Functional Genomics

Abstract

A high-quality NMR structure of the helicase associated (HA) domain comprising residues 627–691 of the 753-residue protein BVU_0683 from Bacteroides vulgatus exhibits an all α-helical fold. The structure presented here is the first representative for the large protein domain family PF03457 (currently 742 members) of HA domains. Comparison with structurally similar proteins supports the hypothesis that HA domains bind to DNA and that binding specificity varies greatly within the family of HA domains constituting PF03457.

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Fig. 1
Fig. 2

Abbreviations

DNA:

Deoxyribonucleic acid

DSS:

4,4-dimethyl-4-silapentane-1-sulfonate sodium salt

DTT:

Dithiothreitol

HA:

Helicase associated

ISW:

Imitation switch

MES:

2-(N-morpholino)ethanesulfonic acid

NESG:

Northeast structural genomics consortium

NOE:

Nuclear overhauser effect

PDB:

Protein data bank

RMSD:

Root mean square deviation

SANT:

SWI3, ADA2, N-CoR, and TFIIIB

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Acknowledgments

We thank R. Belote, C. Ciccosanti, K. Hamilton, and G.V.T. Swapna for helpful discussions and technical support. This work was supported by the National Institutes of Health, grant number: U54 GM094597 (T.S. and G.T.M.).

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Authors and Affiliations

  1. Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY, 14260, USA

    Jeffrey L. Mills & Thomas Szyperski

  2. Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ, 08854, USA

    Thomas B. Acton, Rong Xiao, John K. Everett & Gaetano T. Montelione

  3. Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ, 08854, USA

    Gaetano T. Montelione

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  1. Jeffrey L. Mills
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Correspondence to Thomas Szyperski.

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Mills, J.L., Acton, T.B., Xiao, R. et al. Solution NMR structure of the helicase associated domain BVU_0683(627–691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA. J Struct Funct Genomics 14, 19–24 (2013). https://doi.org/10.1007/s10969-012-9148-0

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