PDBsum entry 1euf

Hydrolase

PDB id: 1euf

Contents

Protein chain

224 a.a. *

Ligands

NAG

PO4

Waters ×69

* Residue conservation analysis

PDB id:

1euf

Name:

Hydrolase

Title:

Bovine duodenase(new serine protease), crystal structure

Structure:

Duodenase. Chain: a. Ec: 3.4.21.-

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: brunner's gland

Resolution:

2.40Å R-factor: 0.179 R-free: 0.223

Authors:

V.Z.Pletnev,T.S.Zamolodchikova,W.A.Pangborn,W.L.Duax

Key ref:

V.Z.Pletnev et al. (2000). Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities. Proteins, 41, 8. PubMed id: 10944388 DOI: 10.1002/1097-0134(20001001)41:1<8::AID-PROT30>3.3.CO;2-U

Date:

14-Apr-00 Release date: 14-Apr-01

Protein chain

P80219  (DDN1_BOVIN) -  Duodenase-1 from Bos taurus

Seq: 251 a.a.

Struc: 224 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1002/1097-0134(20001001)41:1<8::AID-PROT30>3.3.CO;2-U

Proteins 41:8 (2000)

PubMed id: 10944388

Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.

V.Z.Pletnev, T.S.Zamolodchikova, W.A.Pangborn, W.L.Duax.

ABSTRACT

The three-dimensional structure of duodenase, a serine protease from bovine duodenum mucosa, has been determined at 2.4A resolution. The enzyme, which has both trypsin-like and chymotrypsin-like activities, most closely resembles human cathepsin G with which it shares 57% sequence identity and similar specificity. The catalytic Ser195 in duodenase adopts the energetically favored conformation typical of serine proteinases and unlike the strained state typical of lipase/esterases. Of several waters in the active site of duodenase, the one associated with Ser214 is found in all serine proteinases and most lipase/esterases. The conservation of the Ser214 residue in serine proteinase, its presence in the active site, and participation in a hydrogen water network involving the catalytic triad (His57, Asp107, and Ser195) argues for its having an important role in the mechanism of action. It may be referred to as a fourth member of the catalytic triad. Duodenase is one of a growing family of enzymes that possesses trypsin-like and chymotrypsin-like activity. Not long ago, these activities were considered to be mutually exclusive. Computer modeling reveals that the S1 subsite of duodenase has structural features compatible with effective accommodation of P1 residues typical of trypsin (Arg/Lys) and chymotrypsin (Tyr/Phe) substrates. The determination of structural features associated with functional variation in the enzyme family may permit design of enzymes with a specific ratio of trypsin and chymotrypsin activities.

Selected figure(s)

Figure 1.
Figure 1. A ribbon representation of three-dimensional structure of duodenase with catalytic triad His57, Asp102, and Ser195 shown in red and disulfide bonds between residues 42:58, 136:201, and 168:182 in brown. -strands (blue) and helices (magenta) are shown by arrow and helix representation, respectively.

Figure 2.
Figure 2. A scheme of duodenase secondary structure topology. -strand and helix elements are presented by arrows and helices, respectively. Only one hydrogen nonbonded residue in b conformation is allowed for inclusion at -strand termini.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 41, 8-0) copyright 2000.

Figures were selected by the author.