PDBsum entry 1xxd

Blood clotting/hydrolase inhibitor

PDB id: 1xxd

Contents

Protein chains

238 a.a. *

137 a.a. *

Waters ×58

* Residue conservation analysis

PDB id:

1xxd

Name:

Blood clotting/hydrolase inhibitor

Title:

Crystal structure of the fxia catalytic domain in complex with mutated ecotin

Structure:

Coagulation factor xi. Chain: a, b. Fragment: catalytic domain. Synonym: plasma thromboplastin antecedent. Pta. Fxi. Engineered: yes. Mutation: yes. Ecotin. Chain: c, d. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: f11. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Escherichia coli. Organism_taxid: 562. Gene: eco,eti.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.91Å R-factor: 0.230 R-free: 0.282

Authors:

L.Jin,P.Pandey,R.E.Babine,J.C.Gorga,K.J.Seidl,E.Gelfand,D.T.Weaver, S.S.Abdel-Meguid,J.E.Strickler

Key ref:

L.Jin et al. (2005). Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions. J Biol Chem, 280, 4704-4712. PubMed id: 15545266 DOI: 10.1074/jbc.M411309200

Date:

04-Nov-04 Release date: 16-Nov-04

Protein chains

P03951  (FA11_HUMAN) -  Coagulation factor XI from Homo sapiens

Seq: 625 a.a.

Struc: 238 a.a.*

Protein chains

P23827  (ECOT_ECOLI) -  Ecotin from Escherichia coli (strain K12)

Seq: 162 a.a.

Struc: 137 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.21.27 - coagulation factor XIa.
• Reaction: Selective cleavage of Arg-|-Ala and Arg-|-Val bonds in factor IX to form factor IXa.

DOI no: 10.1074/jbc.M411309200

J Biol Chem 280:4704-4712 (2005)

PubMed id: 15545266

Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions.

L.Jin, P.Pandey, R.E.Babine, J.C.Gorga, K.J.Seidl, E.Gelfand, D.T.Weaver, S.S.Abdel-Meguid, J.E.Strickler.

ABSTRACT

Thrombosis can lead to life-threatening conditions such as acute myocardial infarction, pulmonary embolism, and stroke. Although commonly used anti-coagulant drugs, such as low molecular weight heparin and warfarin, are effective, they carry a significant risk of inducing severe bleeding complications, and there is a need for safer drugs. Activated Factor XI (FXIa) is a key enzyme in the amplification phase of the coagulation cascade. Anti-human FXI antibody significantly reduces thrombus growth in a baboon thrombosis model without bleeding problems (Gruber, A., and Hanson, S. R. (2003) Blood 102, 953-955). Therefore, FXIa is a potential target for anti-thrombosis therapy. To determine the structure of FXIa, we derived a recombinant catalytic domain of FXI, consisting of residues 370-607 (rhFXI370-607). Here we report the first crystal structure of rhFXI370-607 in complex with a substitution mutant of ecotin, a panserine protease protein inhibitor secreted by Escherichia coli, to 2.2 A resolution. The presence of ecotin not only assisted in the crystallization of the enzyme but also revealed unique structural features in the active site of FXIa. Subsequently, the sequence from P5 to P2' in ecotin was mutated to the FXIa substrate sequence, and the structures of the rhFXI370-607-ecotin mutant complexes were determined. These structures provide us with an understanding of substrate binding interactions of FXIa, the structural information essential for the structure-based design of FXIa-selective inhibitors.

Selected figure(s)

Figure 1.
FIG. 1. Stereoview of the crystal structure of rhFXI[370-607]-ecotinM84R. A, a C trace of rhFXI[370-607]-ecotinM84R tetramer. The ecotinM84R molecules are colored in blue and yellow, and the rhFXI[370-607] molecules are colored in green and red. The N and C termini of each molecule are labeled in the same color as the molecule. The primary and secondary binding sites between rhFXI[370-607] and ecotinM84R are indicated by arrows. B, a ribbon diagram of the catalytic domain of FXIa in the rhFXI[370-607]-ecotinM84R crystal structure. The helices are colored in purple and sheets are in green. A few key residues, discussed in the text, are presented in a ball-and-stick representation with CPK coloring. The N and C termini are indicated. All figures were prepared with DINO (www.dino3.org) and Povray (www.povray.org).

Figure 3.
FIG. 3. Stereoview of the active site in the rhFXI[370-607]-ecotinM84R structure. rhFXI[370-607] is in a surface representation with the following color scheme: basic residues in blue, acidic residues in red; polar residues in yellow, and all others in white. Residues 78-88 of ecotinM84R, labeled as P[7] to P[4'] are shown as a stick figure with CPK coloring.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 4704-4712) copyright 2005.

Figures were selected by an automated process.