PDBsum entry 1kma

Blood clotting

PDB id: 1kma

Contents

Protein chain

55 a.a. *

* Residue conservation analysis

PDB id:

1kma

Name:

Blood clotting

Title:

Nmr structure of the domain-i of the kazal-type thrombin inhibitor dipetalin

Structure:

Dipetalin. Chain: a. Fragment: n-terminal domain-i. Synonym: dipetalogastin. Engineered: yes

Source:

Dipetalogaster maximus. Organism_taxid: 72496. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

B.Schlott,J.Wohnert,C.Icke,M.Hartmann,R.Ramachandran,K.-H.Guhrs, E.Glusa,J.Flemming,M.Gorlach,F.Grosse,O.Ohlenschlager

Key ref:

B.Schlott et al. (2002). Interaction of Kazal-type inhibitor domains with serine proteinases: biochemical and structural studies. J Mol Biol, 318, 533-546. PubMed id: 12051857 DOI: 10.1016/S0022-2836(02)00014-1

Date:

14-Dec-01 Release date: 15-May-02

Protein chain

O96790  (DPGN_DIPMA) -  Serine protease inhibitor dipetalogastin (Fragment) from Dipetalogaster maximus

Seq: 351 a.a.

Struc: 55 a.a.

DOI no: 10.1016/S0022-2836(02)00014-1

J Mol Biol 318:533-546 (2002)

PubMed id: 12051857

Interaction of Kazal-type inhibitor domains with serine proteinases: biochemical and structural studies.

B.Schlott, J.Wöhnert, C.Icke, M.Hartmann, R.Ramachandran, K.H.Gührs, E.Glusa, J.Flemming, M.Görlach, F.Grosse, O.Ohlenschläger.

ABSTRACT

The interaction of domains of the Kazal-type inhibitor protein dipetalin with the serine proteinases thrombin and trypsin is studied. The functional studies of the recombinantly expressed domains (Dip-I+II, Dip-I and Dip-II) allow the dissection of the thrombin inhibitory properties and the identification of Dip-I as a key contributor to thrombin/dipetalin complex stability and its inhibitory potency. Furthermore, Dip-I, but not Dip-II, forms a complex with trypsin resulting in an inhibition of the trypsin activity directed towards protein substrates. The high resolution NMR structure of the Dip-I domain is determined using multi-dimensional heteronuclear NMR spectroscopy. Dip-I exhibits the canonical Kazal-type fold with a central alpha-helix and a short two-stranded antiparallel beta-sheet. Molecular regions essential for inhibitor complex formation with thrombin and trypsin are identified. A comparison with molecular complexes of other Kazal-type thrombin and trypsin inhibitors by molecular modeling shows that the N-terminal segment of Dip-I fulfills the structural prerequisites for inhibitory interactions with either proteinase and explains the capacity of this single Kazal-type domain to interact with different proteinases.

Selected figure(s)

Figure 2.
Figure 2. Thrombin inhibition by fusion proteins and isolated dipetalin domains. The ordinate gives the relation of the rate constants for substrate turnover by thrombin in the presence of the test compound (v) and by thrombin only (v[0]). The abscissa shows the concentrations of the tested proteins. The lines in blue represent the fusion proteins H[6]-Sak-Dip-I ( open ); H[6]-Sak-Dip-II ( triangle, open ); H[6]-Sak-Dip-I+II (0m); lines in red represent the isolated domains Dip-I ( open ); Dip-II ( triangle, open ); Dip-I+II (0m); the black line represents H[6]-Sak-FXa ( ) and the green line represents the complementation experiment using Dip-I+Dip-II in 1:1 stoichiometric amounts ( ). Error bars are indicated for each measurement.

Figure 4.
Figure 4. [1H-15N] HSQC spectra of dipetalin-I (a) and the trypsin/Dip-I complex (b). In the complexation experiments only Dip-I was labeled with 15N.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 533-546) copyright 2002.

Figures were selected by the author.