1WMF

Crystal Structure of alkaline serine protease KP-43 from Bacillus sp. KSM-KP43 (oxidized form, 1.73 angstrom)

Summary for 1WMF

• Entry DOI: 10.2210/pdb1wmf/pdb
• Related: 1WMD 1WME
• Descriptor: protease, CALCIUM ION, 1,4-DIETHYLENE DIOXIDE, ... (5 entities in total)
• Functional Keywords: alpha-beta hydrolase fold, jelly-roll beta-barrel, hydrolase
• Biological source: Bacillus sp.
• Total number of polymer chains: 1
• Total formula weight: 45671.27

Authors

Nonaka, T.,Fujihashi, M.,Kita, A.,Saeki, K.,Ito, S.,Horikoshi, K.,Miki, K. (deposition date: 2004-07-08, release date: 2004-09-14, Last modification date: 2025-03-26)

Primary citation

Nonaka, T.,Fujihashi, M.,Kita, A.,Saeki, K.,Ito, S.,Horikoshi, K.,Miki, K.
The Crystal Structure of an Oxidatively Stable Subtilisin-like Alkaline Serine Protease, KP-43, with a C-terminal {beta}-Barrel Domain
J.Biol.Chem., 279:47344-47351, 2004

PubMed Abstract: The crystal structure of an oxidatively stable subtilisin-like alkaline serine protease, KP-43 from Bacillus sp. KSM-KP43, with a C-terminal extension domain, was determined by the multiple isomorphous replacements method with anomalous scattering. The native form was refined to a crystallographic R factor of 0.134 (Rfree of 0.169) at 1.30-A resolution. KP-43 consists of two domains, a subtilisin-like alpha/beta domain and a C-terminal jelly roll beta-barrel domain. The topological architecture of the molecule is similar to that of kexin and furin, which belong to the subtilisin-like proprotein convertases, whereas the amino acid sequence and the binding orientation of the C-terminal beta-barrel domain both differ in each case. Since the C-terminal domains of subtilisin-like proprotein convertases are essential for folding themselves, the domain of KP-43 is also thought to play such a role. KP-43 is known to be an oxidation-resistant protease among the general subtilisin-like proteases. To investigate how KP-43 resists oxidizing reagents, the structure of oxidized KP-43 was also determined and refined to a crystallographic R factor of 0.142 (Rfree of 0.212) at 1.73-A resolution. The structure analysis revealed that Met-256, adjacent to catalytic Ser-255, was oxidized similarly to an equivalent residue in subtilisin BPN'. Although KP-43, as well as proteinase K and subtilisin Carlsberg, lose their hydrolyzing activity against synthetic peptides after oxidation treatment, all of them retain 70-80% activity against proteinaceous substrates. These results, as well as the beta-casein digestion pattern analysis, have indicated that the oxidation of the methionine adjacent to the catalytic serine is not a dominant modification but might alter the substrate specificities.

PubMed: 15342641
DOI: 10.1074/jbc.M409089200

Experimental method

X-RAY DIFFRACTION (1.73 Å)