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X-ray Crystal Structure of Divalent Metal-Activated β-xylosidase, RS223BX

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Abstract

We report the X-ray crystal structure of a glycoside hydrolase family 43 β-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca2+ cation is located at the back of the active-site pocket. The Ca2+ is held in the active site by the carboxylate of D85, an “extra” acid residue in comparison to other GH43 active sites. The Ca2+ is in close contact with a histidine imidazole, which in turn is in contact with the catalytic base (D15) thus providing a mechanism for stabilizing the carboxylate anion of the base and achieve metal activation. The active-site pocket is mirrored by an “inactive-site” pocket of unknown function that resides on the opposite side of the monomer.

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Abbreviations

4NPX:

4-nitrophenyl-β-D-xylopyranoside

GH43:

glycoside hydrolase family 43

M2+ :

divalent metal cation

RS223BX:

β-xylosidase of this study

X2:

xylobiose

X3:

xylotriose

X4:

xylotetraose

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Acknowledgments

This work was supported in part by the United States Department of Agriculture CRIS 3620-41000-133-00D (D.B.J. and J.D.B.) and CRIS 5325-41000-049-00 (K.W, C.C.L, and V.J.C). Mention of trade names or commercial products in this report is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

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Authors and Affiliations

  1. USDA-ARS-National Center for Agricultural Utilization Research, 1815 N. University St, Peoria, IL, 61604, USA

    Douglas B. Jordan & Jay D. Braker

  2. USDA-ARS-Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA

    Kurt Wagschal, Charles C. Lee & Victor J. Chan

  3. Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA

    Ievgeniia Dubrovska

  4. Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL, 60439, USA

    Spencer Anderson & Zdzislaw Wawrzak

Authors
  1. Douglas B. Jordan
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  2. Jay D. Braker
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  3. Kurt Wagschal
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  4. Charles C. Lee
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  5. Victor J. Chan
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  6. Ievgeniia Dubrovska
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  7. Spencer Anderson
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  8. Zdzislaw Wawrzak
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Corresponding author

Correspondence to Douglas B. Jordan.

Electronic supplementary material

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ESM 1

A figure of some of the xylotetraose contacts within 4 Å of RS223BX, table of closest residue-residue pair contacts between subunits that are not part of the same dimer and could help form a tetramer, electron density map of a portion of the RS223BX active site, a 3D overlay of the RS223BX (this work) and the arabinanase (PDB ID 2X8F) structures, and an alignment of amino acid sequences of the four GH43 enzymes discussed in this work. (DOCX 1898 kb)

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Jordan, D.B., Braker, J.D., Wagschal, K. et al. X-ray Crystal Structure of Divalent Metal-Activated β-xylosidase, RS223BX. Appl Biochem Biotechnol 177, 637–648 (2015). https://doi.org/10.1007/s12010-015-1767-z

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  • DOI: https://doi.org/10.1007/s12010-015-1767-z

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