Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis

Biochemistry
Marek J KobylarzMichael E P Murphy

Abstract

Staphylococcus aureus assembles the siderophore, staphyloferrin B, from l-2,3-diaminopropionic acid (l-Dap), α-ketoglutarate, and citrate. Recently, SbnA and SbnB were shown to produce l-Dap and α-ketoglutarate from O-phospho-l-serine (OPS) and l-glutamate. SbnA is a pyridoxal 5'-phosphate (PLP)-dependent enzyme with homology to O-acetyl-l-serine sulfhydrylases; however, SbnA utilizes OPS instead of O-acetyl-l-serine (OAS), and l-glutamate serves as a nitrogen donor instead of a sulfide. In this work, we examined how SbnA dictates substrate specificity for OPS and l-glutamate using a combination of X-ray crystallography, enzyme kinetics, and site-directed mutagenesis. Analysis of SbnA crystals incubated with OPS revealed the structure of the PLP-α-aminoacrylate intermediate. Formation of the intermediate induced closure of the active site pocket by narrowing the channel leading to the active site and forming a second substrate binding pocket that likely binds l-glutamate. Three active site residues were identified: Arg132, Tyr152, Ser185 that were essential for OPS recognition and turnover. The Y152F/S185G SbnA double mutant was completely inactive, and its crystal structure revealed that the mutations induced a closed form of ...Continue Reading

References

Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M R Webb
Jul 20, 1990·European Journal of Biochemistry·S Konetschny-RappH Zähner
May 31, 1974·Science·E D Weinberg
Jan 1, 1993·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·H DrechselG Jung
Jun 1, 1996·Microbiology·David E TownsendBrian J Wilkinson
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Oct 12, 2000·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·K ShibataR Yamada
Sep 26, 2002·Journal of Biochemistry and Molecular Biology·Hyeon-Su Ro
Aug 26, 2003·Antimicrobial Agents and Chemotherapy·Michael G ThomasSarah G Ozanick
Jun 11, 2004·Annual Review of Biochemistry·Andrew C Eliot, Jack F Kirsch
May 1, 1997·Acta Crystallographica. Section D, Biological Crystallography·G N MurshudovE J Dodson
Oct 19, 2004·Annual Review of Microbiology·Cécile Wandersman, Philippe Delepelaire
Dec 22, 2005·Acta Crystallographica. Section D, Biological Crystallography·Philip Evans
Mar 23, 2006·Acta Crystallographica. Section D, Biological Crystallography·Jay Painter, Ethan A Merritt
Mar 14, 2007·The Journal of Biological Chemistry·Matthew W BowlerJohn E Walker
May 15, 2007·Applied and Environmental Microbiology·Elizabeth A FelnagleMichael G Thomas
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Thomas C TerwilligerPaul D Adams
Apr 30, 2009·Molecular Microbiology·Federico C BeasleyDavid E Heinrichs
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Sep 25, 2009·Molecular Microbiology·Johnson CheungDavid E Heinrichs
Jan 1, 2010·Journal of Natural Products·Jessica DawlatyJon Clardy
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Gábor Bunkóczi, Randy J Read
Apr 29, 2011·PloS One·Natalia MalachowaFrank R DeLeo
Jun 7, 2011·Annual Review of Microbiology·Neal D Hammer, Eric P Skaar

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Citations

Jun 15, 2019·The Journal of Biological Chemistry·Meghan M VerstraeteMichael E P Murphy
Apr 5, 2020·International Journal of Molecular Sciences·Marialaura MarchettiLuca Ronda
Jun 3, 2020·Nature Chemical Biology·Zheng CuiSteven G Van Lanen
Feb 28, 2018·The Journal of Biological Chemistry·Meghan M VerstraeteMichael E P Murphy
Mar 27, 2019·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·Brigid S ConroyMichael E P Murphy
Apr 26, 2020·Communications Biology·Zhi-Wei LiXiao-Chun Luo
Jun 5, 2021·Accounts of Chemical Research·Duncan J Kountz, Emily P Balskus
Sep 14, 2017·The Journal of Organic Chemistry·Sandip SenguptaTaebo Sim
Dec 24, 2019·Chemical Reviews·Jason B Hedges, Katherine S Ryan

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Methods Mentioned

BETA
PCR
dynamic light scattering
size
light scattering
static light scattering
PISA
X-ray

Software Mentioned

BLAST
CCP4
Scala
Coot
Graphpad Prism
phenix
ASTRA6
Phaser
Refmac
Mosflm

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