1K20

Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution

Summary for 1K20

• Entry DOI: 10.2210/pdb1k20/pdb
• Related: 1K23
• Descriptor: Manganese-dependent inorganic pyrophosphatase, MANGANESE (II) ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: family ii ppase, manganese, binuclear metal centre, hydrolase
• Biological source: Streptococcus gordonii
• Cellular location: Cytoplasm (By similarity): P95765
• Total number of polymer chains: 2
• Total formula weight: 67755.13

Authors

Ahn, S.,Milner, A.J.,Futterer, K.,Konopka, M.,Ilias, M.,Young, T.W.,White, S.A. (deposition date: 2001-09-26, release date: 2001-10-31, Last modification date: 2024-02-07)

Primary citation

Ahn, S.,Milner, A.J.,Futterer, K.,Konopka, M.,Ilias, M.,Young, T.W.,White, S.A.
The "open" and "closed" structures of the type-C inorganic pyrophosphatases from Bacillus subtilis and Streptococcus gordonii.
J.Mol.Biol., 313:797-811, 2001

PubMed Abstract: Recently, a new class of soluble inorganic pyrophosphatase (type-C PPase) has been described that is not homologous in amino acid sequence or kinetic properties to the well-studied PPases (types A and B) found in many organisms from bacteria to humans and thought to be essential to the cell. Structural studies of the type-C PPases from Streptococcus gordonii and Bacillus subtilis reveal a homodimeric structure, with each polypeptide folding into two domains joined by a flexible hinge. The active site, formed at the interface between the N and C-terminal domains, binds two manganese ions approximately 3.6 A apart in a conformation resembling binuclear metal centres found in other hydrolytic enzymes. An activated water molecule bridging the two metal ions is likely poised for nucleophilic attack of the substrate. Importantly, the S. gordonii and B. subtilis enzymes have crystallised in strikingly different conformations. In both subunits of the S. gordonii crystal structure (1.5 A resolution) the C-terminal domain is positioned such that the active site is occluded, with a sulphate ion bound in the active site. In contrast, in the B. subtilis structure (3.0 A resolution) the C-terminal domain is rotated by about 90 degrees, leaving the active site wide open and accessible for substrate binding.

PubMed: 11697905
DOI: 10.1006/jmbi.2001.5070

Experimental method

X-RAY DIFFRACTION (1.5 Å)