PDBsum entry 1yu6

Hydrolase

PDB id: 1yu6

Contents

Protein chains

274 a.a. *

51 a.a. *

Metals

_CA ×2

Waters ×329

* Residue conservation analysis

PDB id:

1yu6

Name:

Hydrolase

Title:

Crystal structure of the subtilisin carlsberg:omtky3 complex

Structure:

Subtilisin carlsberg. Chain: a, b. Ovomucoid. Chain: c, d. Engineered: yes

Source:

Bacillus licheniformis. Organism_taxid: 1402. Meleagris gallopavo. Turkey. Organism_taxid: 9103. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.55Å R-factor: 0.192 R-free: 0.205

Authors:

J.T.Maynes,M.M.Cherney,M.A.Qasim,M.Laskowski Jr.,M.N.G.James

Key ref:

J.T.Maynes et al. (2005). Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations. Acta Crystallogr D Biol Crystallogr, 61, 580-588. PubMed id: 15858268 DOI: 10.1107/S0907444905004889

Date:

11-Feb-05 Release date: 03-May-05

Protein chains

P00780  (SUBC_BACLI) -  Subtilisin Carlsberg from Bacillus licheniformis

Seq: 379 a.a.

Struc: 274 a.a.*

Protein chains

P68390  (IOVO_MELGA) -  Ovomucoid from Meleagris gallopavo

Seq: 185 a.a.

Struc: 51 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.21.62 - subtilisin.
• Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.

DOI no: 10.1107/S0907444905004889

Acta Crystallogr D Biol Crystallogr 61:580-588 (2005)

PubMed id: 15858268

Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.

J.T.Maynes, M.M.Cherney, M.A.Qasim, M.Laskowski, M.N.James.

ABSTRACT

One of the most studied protein proteinase inhibitors is the turkey ovomucoid third domain, OMTKY3. This inhibitor contains a reactive-site loop (Lys13I-Arg21I) that binds in a nearly identical manner to all studied serine proteinases, regardless of their clan or specificity. The crystal structure of OMTKY3 bound to subtilisin Carlsberg (CARL) has been determined. There are two complete copies of the complexes in the crystallographic asymmetric unit. Whereas the two enzyme molecules are virtually identical [0.16 A root-mean-square difference (r.m.s.d.) for 274 C(alpha) atoms], the two inhibitor molecules show dramatic differences between one another (r.m.s.d. = 2.4 A for 50 C(alpha) atoms). When compared with other proteinase-bound OMTKY3 molecules, these inhibitors show even larger differences. This work facilitates a re-evaluation of the importance of certain ovomucoid residues in proteinase binding and explains why additivity and sequence-based binding-prediction methods fail for the CARL-OMTKY3 complex.

Selected figure(s)

Figure 3.
Figure 3 (a) Active-site representation of one of the CARL-OMKTY3 complexes in the asymmetric unit. C atoms for the CARL structure are colored orange and for OMTKY3 are colored grey. Labelling for pertinent residues follows a similar coloring scheme. Water molecules are shown as green spheres and hydrogen-bonding interactions are shown as dashed lines. (b) Active-site representation of the second complex of CARL-OMTKY3 present in the asymmetric unit. Coloring is as in (a). (c) Representative electron density shown in stereo for the catalytic triad of subtilisin (Asp32, His64 and Ser221) and the P[2] (Thr17I), P[1] (Leu18I) and [134][{\rm P}'_{1}] (Glu19I) residues of the ovomucoid inhibitor. The map shown is a [135][sigma] [A]-weighted 2|F[o]| - |F[c]| map ( [136][alpha] [calc]) contoured at 1 [137][sigma] .

Figure 4.
Figure 4 Overlay of the complex between CARL-OMTKY3 and CARL-eglin c (PDB code [208]1cse ). The CARL-OMTKY3 complex is shown with orange (CARL) and blue (OMKTY) C atoms. The CARL-eglin c complex is shown with green (CARL) and yellow (eglin c) C atoms. The sequence of OMKTY3 in this region is P[2]-Thr-Leu-Glu- [209][{\rm P}'_{1}] and for eglin c the sequence is P[2]-Thr-Leu-Asp- [210][{\rm P}'_{1}] . Potential hydrogen bonds are shown as dashed lines.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 580-588) copyright 2005.

Figures were selected by the author.