PDBsum entry 1eb6

Hydrolase

PDB id: 1eb6

Contents

Protein chain

177 a.a. *

Ligands

EDO ×3

Metals

_ZN

Waters ×259

* Residue conservation analysis

PDB id:

1eb6

Name:

Hydrolase

Title:

Deuterolysin from aspergillus oryzae

Structure:

Neutral protease ii. Chain: a. Synonym: npii, deuterolysin. Ec: 3.4.24.39

Source:

Aspergillus oryzae. Organism_taxid: 5062

Resolution:

1.00Å R-factor: 0.104 R-free: 0.126

Authors:

K.E.Mcauley,Y.Jia-Xing,E.J.Dodson,J.Lehmbeck,P.R.Ostergaard, K.S.Wilson

Key ref:

K.E.McAuley et al. (2001). A quick solution: ab initio structure determination of a 19 kDa metalloproteinase using ACORN. Acta Crystallogr D Biol Crystallogr, 57, 1571-1578. PubMed id: 11679721 DOI: 10.1107/S090744490101335X

Date:

19-Jul-01 Release date: 23-Nov-01

Protein chain

P46076  (NPII_ASPOR) -  Neutral protease 2 from Aspergillus oryzae (strain ATCC 42149 / RIB 40)

Seq: 352 a.a.

Struc: 177 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.24.39 - deuterolysin.
• Reaction: Preferential cleavage of bonds with hydrophobic residues in P1'; also 3-Asn-|-Gln-4 and 8-Gln-|-Ser-9 bonds in insulin B chain.
• Cofactor: Zn(2+)

DOI no: 10.1107/S090744490101335X

Acta Crystallogr D Biol Crystallogr 57:1571-1578 (2001)

PubMed id: 11679721

A quick solution: ab initio structure determination of a 19 kDa metalloproteinase using ACORN.

K.E.McAuley, Y.Jia-Xing, E.J.Dodson, J.Lehmbeck, P.R.Østergaard, K.S.Wilson.

ABSTRACT

A data set from the metalloproteinase deuterolysin was collected at atomic resolution (1.0 A) with synchrotron radiation. The high resolution allowed the structure to be solved with the new direct-methods program ACORN using the coordinates of the Zn atom as a starting point. The phases obtained from ACORN were of sufficient quality to allow automated building to be carried out in ARP/wARP. Minimal manual rebuilding of the model was required and the structure determination was completed using the maximum-likelihood refinement program REFMAC. The whole process, starting from the processed and merged data and ending with a refined model, required less than 6 h of computational time.

Selected figure(s)

Figure 1.
Figure 1 v = 0.5 Harker sections of (a) the anomalous difference and (b) the sharpened native Patterson functions.

Figure 5.
Figure 5 Comparison of the metalloproteinases (a) snapalysin (PDB code [148]1kuh ), (b) astacin (PDB code [149]1iab ), (c) deuterolysin, (d) leishmanolysin (PDB code [150]1lml ) and (e) thermolysin (PDB code [151]2tmn ). The matching secondary-structure elements are shown as either cylinders (for helices) or arrows (for sheets) and the remainder of the protein is shown as a smoothed C^ [152][alpha] trace.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1571-1578) copyright 2001.

Figures were selected by an automated process.