PDBsum entry 1rfn

Coagulation factor

PDB id: 1rfn

Contents

Protein chains

235 a.a. *

57 a.a. *

Ligands

PBZ

TBU

Metals

_CA

Waters ×16

* Residue conservation analysis

PDB id:

1rfn

Name:

Coagulation factor

Title:

Human coagulation factor ixa in complex with p-amino benzamidine

Structure:

Protein (coagulation factor ix). Chain: a. Fragment: fragment egf2-catalytic domain. Engineered: yes. Protein (coagulation factor ix). Chain: b. Fragment: fragment egf2-catalytic domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.216 R-free: 0.273

Authors:

K.-P.Hopfner,A.Lang,A.Karcher,K.Sichler,E.Kopetzki,H.Brandstetter, R.Huber,W.Bode,R.A.Engh

Key ref:

K.P.Hopfner et al. (1999). Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding. Structure, 7, 989-996. PubMed id: 10467148 DOI: 10.1016/S0969-2126(99)80125-7

Date:

19-Apr-99 Release date: 01-Sep-99

Protein chain

P00740  (FA9_HUMAN) -  Coagulation factor IX from Homo sapiens

Seq: 461 a.a.

Struc: 235 a.a.

Protein chain

P00740  (FA9_HUMAN) -  Coagulation factor IX from Homo sapiens

Seq: 461 a.a.

Struc: 57 a.a.*

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

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.21.22 - coagulation factor IXa.
• Reaction: Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.

DOI no: 10.1016/S0969-2126(99)80125-7

Structure 7:989-996 (1999)

PubMed id: 10467148

Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding.

K.P.Hopfner, A.Lang, A.Karcher, K.Sichler, E.Kopetzki, H.Brandstetter, R.Huber, W.Bode, R.A.Engh.

ABSTRACT

BACKGROUND: Among the S1 family of serine proteinases, the blood coagulation factor IXa (fIXa) is uniquely inefficient against synthetic peptide substrates. Mutagenesis studies show that a loop of residues at the S2-S4 substrate-binding cleft (the 99-loop) contributes to the low efficiency. The crystal structure of porcine fIXa in complex with the inhibitor D-Phe-Pro-Arg-chloromethylketone (PPACK) was unable to directly clarify the role of the 99-loop, as the doubly covalent inhibitor induced an active conformation of fIXa. RESULTS: The crystal structure of a recombinant two-domain construct of human fIXa in complex with p-aminobenzamidine shows that the Tyr99 sidechain adopts an atypical conformation in the absence of substrate interactions. In this conformation, the hydroxyl group occupies the volume corresponding to the mainchain of a canonically bound substrate P2 residue. To accommodate substrate binding, Tyr99 must adopt a higher energy conformation that creates the S2 pocket and restricts the S4 pocket, as in fIXa-PPACK. The energy cost may contribute significantly to the poor K(M) values of fIXa for chromogenic substrates. In homologs, such as factor Xa and tissue plasminogen activator, the different conformation of the 99-loop leaves Tyr99 in low-energy conformations in both bound and unbound states. CONCLUSIONS: Molecular recognition of substrates by fIXa seems to be determined by the action of the 99-loop on Tyr99. This is in contrast to other coagulation enzymes where, in general, the chemical nature of residue 99 determines molecular recognition in S2 and S3-S4. This dominant role on substrate interaction suggests that the 99-loop may be rearranged in the physiological fX activation complex of fIXa, fVIIIa, and fX.

Selected figure(s)

Figure 3.
Figure 3. Stereoview comparisons of substrate recognition by fIXa and other homologs. (a) The divergent structures of the fIXa 99-loop (yellow) compared with those of factor Xa (white) and tPA (red) place Tyr99 either in a relaxed position that blocks substrate binding in the S2 site (thick lines) or in a strained position that blocks the S4 site (thin lines). The inhibitor (purple, Image -Phe-Pro-Arg with proline atoms omitted for clarity) position is taken from the superposition of porcine fIXa. (b) The conformation of the fIXa 99-loop (yellow) is stabilized by a hydrogen bond between Tyr94 (phenylalanine in fXa) and Lys98, whereas the fXa 99-loop (gray) conformation is prevented by the position of Tyr177 (threonine in fXa).

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 989-996) copyright 1999.

Figure was selected by an automated process.