1EE6

CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.

Summary for 1EE6

• Entry DOI: 10.2210/pdb1ee6/pdb
• Descriptor: PECTATE LYASE, CALCIUM ION (3 entities in total)
• Functional Keywords: parallel beta-helix, high-alkaline, low-molecular-weight, lyase
• Biological source: Bacillus sp.
• Total number of polymer chains: 1
• Total formula weight: 20987.37

Authors

Akita, M.,Suzuki, A.,Kobayashi, T.,Ito, S.,Yamane, T. (deposition date: 2000-01-31, release date: 2001-01-31, Last modification date: 2024-10-30)

Primary citation

Akita, M.,Suzuki, A.,Kobayashi, T.,Ito, S.,Yamane, T.
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
Acta Crystallogr.,Sect.D, 57:1786-1792, 2001

PubMed Abstract: The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.

PubMed: 11717490
DOI: 10.1107/S0907444900003334

Experimental method

X-RAY DIFFRACTION (2.3 Å)