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De novo calcium/sulfur SAD phasing of the human formylglycine-generating enzyme using in-house data.

Roeser D, Dickmanns A, Gasow K, Rudolph MG
Acta Crystallogr D Biol Crystallogr 61 1057-66 (2005)
Cited: 10 times
EuropePMC logo PMID: 16041070

Abstract

Sulfatases are a family of enzymes essential for the degradation of sulfate esters. Formylglycine is the key catalytic residue in the active site of sulfatases and is generated from a cysteine residue by FGE, the formylglycine-generating enzyme. Inactivity of FGE owing to inherited mutations in the FGE gene results in multiple sulfatase deficiency (MSD), which leads to early death in infants. Human FGE was crystallized in the presence of traces of the protease elastase, which was absolutely essential for crystal growth, and the structure of FGE was determined by molecular replacement. Before this model was completed, the FGE structure was re-determined by SAD phasing using in-house data based on the anomalous signal of two calcium ions bound to the native enzyme and intrinsic S atoms. A 14-atom substructure was determined at 1.8 A resolution by SHELXD; SHELXE was used for density modification and phase extension to 1.54 A resolution. Automated model building with ARP/wARP and refinement with REFMAC5 yielded a virtually complete model without manual intervention. The minimal data requirements for successful phasing and the relative contributions of the Ca and S atoms are discussed and compared with the related FGE paralogue, pFGE. This work emphasizes the usefulness of de novo phasing using weak anomalous scatterers and in-house data.

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  1. Natural disease history and characterisation of SUMF1 molecular defects in ten unrelated patients with multiple sulfatase deficiency. Sabourdy F, Mourey L, Le Trionnaire E, Bednarek N, Caillaud C, Chaix Y, Delrue MA, Dusser A, Froissart R, Garnotel R, Guffon N, Megarbane A, Ogier de Baulny H, Pédespan JM, Pichard S, Valayannopoulos V, Verloes A, Levade T. Orphanet J Rare Dis 10 31 (2015)
  2. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)


Reviews citing this publication (1)

  1. Formylglycine, a post-translationally generated residue with unique catalytic capabilities and biotechnology applications. Appel MJ, Bertozzi CR. ACS Chem Biol 10 72-84 (2015)

Articles citing this publication (7)

  1. A general binding mechanism for all human sulfatases by the formylglycine-generating enzyme. Roeser D, Preusser-Kunze A, Schmidt B, Gasow K, Wittmann JG, Dierks T, von Figura K, Rudolph MG. Proc Natl Acad Sci U S A 103 81-86 (2006)
  2. Reconstitution of Formylglycine-generating Enzyme with Copper(II) for Aldehyde Tag Conversion. Holder PG, Jones LC, Drake PM, Barfield RM, Bañas S, de Hart GW, Baker J, Rabuka D. J Biol Chem 290 15730-15745 (2015)
  3. Phasing macromolecular structures with UV-induced structural changes. Nanao MH, Ravelli RB. Structure 14 791-800 (2006)
  4. Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model. Meyer PA, Ye P, Zhang M, Suh MH, Fu J. Structure 14 973-982 (2006)
  5. In-house zinc SAD phasing at Cu Kα edge. Kim MK, Lee S, An YJ, Jeong CS, Ji CJ, Lee JW, Cha SS. Mol Cells 36 74-81 (2013)
  6. Crystallization and preliminary characterization of the Thermus thermophilus RNA helicase Hera C-terminal domain. Rudolph MG, Wittmann JG, Klostermeier D. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 248-252 (2009)
  7. Phasing with calcium at home. Guo S, Campbell R, Davies PL, Allingham JS. Acta Crystallogr F Struct Biol Commun 75 377-384 (2019)


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