PDBsum entry 2i9a

Hydrolase

PDB id: 2i9a

Contents

Protein chains

123 a.a. *

Ligands

PO4 ×4

Waters ×361

* Residue conservation analysis

PDB id:

2i9a

Name:

Hydrolase

Title:

Crystal structure of the free aminoterminal fragment of urokinase type plasminogen activator (atf)

Structure:

Urokinase-type plasminogen activator. Chain: a, b, c, d. Fragment: n-terminal fragment of urokinase, residues 21-163. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: plau. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227.

Resolution:

1.90Å R-factor: 0.183 R-free: 0.208

Authors:

J.Lubkowski,C.Barinka

Key ref:

C.Barinka et al. (2006). Structural basis of interaction between urokinase-type plasminogen activator and its receptor. J Mol Biol, 363, 482-495. PubMed id: 16979660 DOI: 10.1016/j.jmb.2006.08.063

Date:

05-Sep-06 Release date: 28-Nov-06

Protein chains

P00749  (UROK_HUMAN) -  Urokinase-type plasminogen activator from Homo sapiens

Seq: 431 a.a.

Struc: 123 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.21.73 - u-plasminogen activator.
• Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.

DOI no: 10.1016/j.jmb.2006.08.063

J Mol Biol 363:482-495 (2006)

PubMed id: 16979660

Structural basis of interaction between urokinase-type plasminogen activator and its receptor.

C.Barinka, G.Parry, J.Callahan, D.E.Shaw, A.Kuo, K.Bdeir, D.B.Cines, A.Mazar, J.Lubkowski.

ABSTRACT

Recent studies indicate that binding of the urokinase-type plasminogen activator (uPA) to its high-affinity receptor (uPAR) orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes, including wound healing, angiogenesis, inflammation, and cancer metastasis. However, notwithstanding the wealth of biochemical data available describing the activities of uPAR, little is known about the exact mode of uPAR/uPA interactions or the presumed conformational changes that accompany uPA/uPAR engagement. Here, we report the crystal structure of soluble urokinase plasminogen activator receptor (suPAR), which contains the three domains of the wild-type receptor but lacks the cell-surface anchoring sequence, in complex with the amino-terminal fragment of urokinase-type plasminogen activator (ATF), at the resolution of 2.8 A. We report the 1.9 A crystal structure of free ATF. Our results provide a structural basis, represented by conformational changes induced in uPAR, for several published biochemical observations describing the nature of uPAR/uPA interactions and provide insight into mechanisms that may be responsible for the cellular responses induced by uPA binding.

Selected figure(s)

Figure 2.
Figure 2. A representation of ATF binding to uPAR. Domains D^I (amino acid residues 1–93), D^II (residues 94–191) and D^III (residues 192–277) of suPAR are shown in yellow, blue, and red, respectively; KD (residues 47–132) is in green, GFD (residues 10–46) in magenta. (a) A cartoon representation of the suPAR[2345]/ATF complex. The individual β-strands of suPAR[2345] are labeled according to Llinas et al.^30 and Low et al.^31 Domain D^I: βIA (residues 2–8), βIB (13–17), βIC (24–33), βID (38–45), βIE (53–59), and βIF (63–70); domain D^II: βIIA (94–100), βIIB (112–115), βIIC (122–129), βIID (143–149), βIIE (156–161), and βIIF (163–171); domain D^III: βIIIA (195–199), βIIIB (211–214), βIIIC (222–229), βIIID (236–243), and βIIIE (259–267). Contacts between the domains are mediated via interactions βIE and βIID (domains D^I and D^II), βIIE and βIIID (domains D^II and D^III). (b) The ATF (cartoon representation) binds to the central cavity of suPAR[2345] (surface representation) and the Ω-loop (Cys19–Cys31, ball-and-sticks) is primarily responsible for the high-affinity binding. Residues of suPAR[2345] interacting with ATF are in cyan.

Figure 5.
Figure 5. Repositioning of the “integrin-interacting” loop (Trp129–Arg142) in suPAR[2345] upon ATF binding. Interactions between amino acid residues Cys19–Lys23 of the ATF and Pro138–Asp140 of suPAR[2345] leads to bending of the loop towards the central cavity of the receptor. (a) The complexes, suPAR[2345]/ATF (domains D^I, D^II and D^III colored yellow, blue and red, respectively) and suPAR/AE147 (shown in gray), were aligned on the basis of the corresponding C^α atoms of domain D^I only. GFD is shown as a combination of ball-and-sticks and semi-transparent surface. The βIIC-βIID hairpin is in cartoon representation and its residues interacting with GFD as ball-and-sticks. (b) A detailed view of residues engaged in the interactions between strands βIIC and βIID of suPAR[2345] and the Ω-loop of ATF. The Ω-loop is shown in surface representation and the interacting residues contributed by domain D^II are shown as balls-and-sticks. Note the major movement of the βIIC-βIID hairpin caused by interactions with the Ω-loop. In both structures, amino acid residues 132 through 136 of suPAR are missing.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 363, 482-495) copyright 2006.

Figures were selected by an automated process.