PDBsum entry 3dyb

Hydrolase

PDB id: 3dyb

Contents

Protein chain

279 a.a. *

Ligands

ADA-ADA

EPE

Metals

_CA ×2

Waters ×379

* Residue conservation analysis

PDB id:

3dyb

Name:

Hydrolase

Title:

Proteinase k- digalacturonic acid complex

Structure:

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

Source:

Engyodontium album. Organism_taxid: 37998

Resolution:

1.32Å R-factor: 0.160 R-free: 0.207

Authors:

S.B.Larson,J.S.Day,A.Mcpherson,R.Cudney,C.Nguyen,Center For High- Throughput Structural Biology (Chtsb)

Key ref:

S.B.Larson et al. (2009). High-resolution structure of proteinase K cocrystallized with digalacturonic acid. Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 192-198. PubMed id: 19255463

Date:

25-Jul-08 Release date: 07-Oct-08

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.

Acta Crystallogr Sect F Struct Biol Cryst Commun 65:192-198 (2009)

PubMed id: 19255463

High-resolution structure of proteinase K cocrystallized with digalacturonic acid.

S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, A.McPherson.

ABSTRACT

Proteinase K, a subtilisin-like fungal protease, was crystallized from a cocktail of small molecules containing digalacturonic acid (DGA). The crystal structure was determined to 1.32 A resolution and refined to an R factor of 0.158. The final model contained, beside the protein, two calcium ions, 379 water molecules, a molecule of DGA and a partially occupied HEPES molecule. The DGA molecule has one sugar moiety disposed exactly on a crystallographic twofold axis; the second ring was not observed. The DGA molecule is bound to two protein molecules across the twofold axis through hydrogen-bonding networks involving Ser150 and water molecules. One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions.