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Journal of Bacteriology, November 2009, p. 6936-6949, Vol. 191, No. 22
0021-9193/09/$08.00+0     doi:10.1128/JB.00287-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Zinc-Independent Folate Biosynthesis: Genetic, Biochemical, and Structural Investigations Reveal New Metal Dependence for GTP Cyclohydrolase IB {triangledown} ,{ddagger}

Banumathi Sankaran,1 Shilah A. Bonnett,2 Kinjal Shah,3,¶ Scott Gabriel,4 Robert Reddy,5,§ Paul Schimmel,5 Dmitry A. Rodionov,6 Valérie de Crécy-Lagard,7 John D. Helmann,4 Dirk Iwata-Reuyl,2* and Manal A. Swairjo3*

The Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720,1 Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207,2 Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E. 2nd Street, Pomona, California 91766-1854,3 Department of Microbiology, Cornell University, 327 Wing Hall, Ithaca, New York 14853-8101,4 Departments of Chemistry and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., BCC-379, La Jolla, California 92037,5 Burnham Institute for Medical Research, 10901 N. Torrey Pines Rd., La Jolla, California 92037,6 Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-07007

Received 4 March 2009/ Accepted 14 September 2009

GTP cyclohydrolase I (GCYH-I) is an essential Zn2+-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in Bacteria and Archaea, and the biopterin pathway in mammals. We recently reported the discovery of a new prokaryotic-specific GCYH-I (GCYH-IB) that displays no sequence identity to the canonical enzyme and is present in ~25% of bacteria, the majority of which lack the canonical GCYH-I (renamed GCYH-IA). Genomic and genetic analyses indicate that in those organisms possessing both enzymes, e.g., Bacillus subtilis, GCYH-IA and -IB are functionally redundant, but differentially expressed. Whereas GCYH-IA is constitutively expressed, GCYH-IB is expressed only under Zn2+-limiting conditions. These observations are consistent with the hypothesis that GCYH-IB functions to allow folate biosynthesis during Zn2+ starvation. Here, we present biochemical and structural data showing that bacterial GCYH-IB, like GCYH-IA, belongs to the tunneling-fold (T-fold) superfamily. However, the GCYH-IA and -IB enzymes exhibit significant differences in global structure and active-site architecture. While GCYH-IA is a unimodular, homodecameric, Zn2+-dependent enzyme, GCYH-IB is a bimodular, homotetrameric enzyme activated by a variety of divalent cations. The structure of GCYH-IB and the broad metal dependence exhibited by this enzyme further underscore the mechanistic plasticity that is emerging for the T-fold superfamily. Notably, while humans possess the canonical GCYH-IA enzyme, many clinically important human pathogens possess only the GCYH-IB enzyme, suggesting that this enzyme is a potential new molecular target for antibacterial development.

* Corresponding author. Mailing address for D. Iwata-Reuyl: Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207. Phone: (503) 725-5737. Fax: (503) 725-9525. E-mail: iwatareuyld{at}pdx.edu. Present address for M. A. Swairjo: Burnham Institute for Medical Research, 10901 N. Torrey Pines Rd., La Jolla, CA 92037. Phone: (619) 206-3864. Fax: (858) 795-5230. E-mail: mswairjo{at}burnham.org

{triangledown} Published ahead of print on 18 September 2009.

{ddagger} Supplemental material for this article may be found at http://jb.asm.org/.

Present address: Long Beach Public Health Lab, 2525 Grand Ave., Room 260, Long Beach, CA 90815.

§ Present address: Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121-2804.

Journal of Bacteriology, November 2009, p. 6936-6949, Vol. 191, No. 22
0021-9193/09/$08.00+0     doi:10.1128/JB.00287-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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