4rpa

From Proteopedia

Crystal structure of inorganic pyrophosphatase from Staphylococcus aureus in complex with Mn2+

PDB ID 4rpa

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Structural highlights

4rpa is a 2 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPAC_STAAM

Publication Abstract from PubMed

Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg2+-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn2+-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn2+ at 2.1A resolution. The active site contains two catalytic Mn2+ binding sites, each half-occupied, reconciling the previously observed 1:1 Mn2+:enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme.

Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.,Gajadeera CS, Zhang X, Wei Y, Tsodikov OV J Struct Biol. 2015 Jan 7. pii: S1047-8477(14)00277-9. doi:, 10.1016/j.jsb.2014.12.003. PMID:25576794^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gajadeera CS, Zhang X, Wei Y, Tsodikov OV. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site. J Struct Biol. 2015 Jan 7. pii: S1047-8477(14)00277-9. doi:, 10.1016/j.jsb.2014.12.003. PMID:25576794 doi:http://dx.doi.org/10.1016/j.jsb.2014.12.003