PDBsum entry 1v47

Transferase

PDB id: 1v47

Contents

Protein chains

346 a.a. *

Ligands

ADX ×2

Metals

_ZN ×2

_CL ×5

_NA ×4

Waters ×164

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Crystal structure of a novel zinc-Binding ATP sulfurylase from thermus thermophilus hb8.
• Authors: Y.Taguchi, M.Sugishima, K.Fukuyama.
• Ref.: Biochemistry, 2004, 43, 4111-4118. [DOI no: 10.1021/bi036052t]
• PubMed id: 15065853

Abstract

ATP sulfurylase (ATPS) is a ubiquitous enzyme that catalyzes the transfer of the adenylyl group from ATP to inorganic sulfate, producing adenosine 5'-phosphosulfate (APS) and pyrophosphate. The crystal structure of ATPS from Thermus thermophilus HB8 (TtATPS, 347 amino acid residues) in complex with APS was determined at 2.5 A resolution. TtATPS is composed of three domains [domain I (residues 1-134), domain II (residues 135-290), and domain III (residues 291-347)], like the Riftia pachyptila symbiont ATPS, but lacks a fourth domain present in ATPSs from the yeast Saccharomyces cerevisiae and from the fungus Penicillium chrysogenum. TtATPS forms a dimer in the crystal, and the manner of subunit association is different from that observed in dimeric R. pachyptila symbiont ATPS and in the hexameric S. cerevisiae and P. chrysogenum ATPSs. APS is located in the active site of TtATPS, which contains several motifs (QXRN, HXXH, and GRD) conserved in ATPSs. Unexpectedly, TtATPS binds one metal ion per subunit in domain III. XAFS measurement of the crystal and the Bijvoet difference Fourier map unambiguously characterized the metal ion as a zinc ion. The zinc ion is tetrahedrally coordinated by Cys294, Cys297, Cys306, and His310, and could not be removed from the protein by treatment with EDTA. The zinc ion binding site is far from the active site. Because all four residues coordinated to the zinc ion are conserved in the ATPSs from thermophilic bacteria such as Archaeoglobus fulgidus, Pyrococcus abyssi, and Sulfolobus solfataricus, zinc ion chelation may contribute to the thermal stability of these ATPSs.

Secondary reference #1

• Title: Overproduction, Crystallization and preliminary X-Ray diffraction analysis of probable ATP sulfurylase from thermus thermophilus hb8.
• Authors: Y.Taguchi, J.Hoseki, Y.Kakuta, K.Fukuyama.
• Ref.: Acta Crystallogr D Biol Crystallogr, 2003, 59, 1645-1647. [DOI no: 10.1107/S0907444903014641]
• PubMed id: 12925800

Figure 3.
Figure 3 Diffraction pattern of the ttATPS crystal. The frame edge is at 2.5 Å resolution.

The above figure is reproduced from the cited reference with permission from the IUCr