PDBsum entry 5kxu

Hydrolase

PDB id: 5kxu

Contents

Protein chain

279 a.a.

Ligands

NO3

Metals

_CA ×2

Waters ×219

PDB id:

5kxu

Name:

Hydrolase

Title:

Structure proteinase k determined by sacla

Structure:

Proteinase k. Chain: a. Synonym: endopeptidase k,tritirachium alkaline proteinase. Ec: 3.4.21.64

Source:

Engyodontium album. Organism_taxid: 37998. Other_details: sigma-aldrich (p2308)

Resolution:

1.20Å R-factor: 0.113 R-free: 0.129

Authors:

T.Masuda,M.Suzuki,S.Inoue,K.Numata,M.Sugahara

Key ref:

T.Masuda et al. (2017). Atomic resolution structure of serine protease proteinase K at ambient temperature. Sci Rep, 7, 45604. PubMed id: 28361898

Date:

20-Jul-16 Release date: 07-Jun-17

Protein chain

P06873  (PRTK_PARAQ) -  Proteinase K from Parengyodontium album

Seq: 384 a.a.

Struc: 279 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.21.64 - peptidase K.
• Reaction: Hydrolysis of keratin and of other proteins, with subtilisin-like specificity. Hydrolyzes peptides amides.

Sci Rep 7:45604 (2017)

PubMed id: 28361898

Atomic resolution structure of serine protease proteinase K at ambient temperature.

T.Masuda, M.Suzuki, S.Inoue, C.Song, T.Nakane, E.Nango, R.Tanaka, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, B.Mikami, O.Nureki, K.Numata, S.Iwata, M.Sugahara.

ABSTRACT

Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.