PDBsum entry 3eif

Hydrolase

PDB id: 3eif

Contents

Protein chain

936 a.a. *

Ligands

SO4 ×7

EPE

MLA

Metals

_CA

_NA

Waters ×917

* Residue conservation analysis

PDB id:

3eif

Name:

Hydrolase

Title:

1.9 angstrom crystal structure of the active form of the c5a peptidase from streptococcus pyogenes (scpa)

Structure:

C5a peptidase. Chain: a. Fragment: residues 67-1002. Synonym: scpa. Engineered: yes. Mutation: yes

Source:

Streptococcus pyogenes. Organism_taxid: 1314. Strain: b220. Gene: scpa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.191 R-free: 0.223

Authors:

J.C.Cooney,T.F.Kagawa,M.R.O'Connell,M.Paoli,P.Mouat,P.W.O'Toole

Key ref:

T.F.Kagawa et al. (2009). Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9-A Crystal Structure of the Active Form of ScpA. J Mol Biol, 386, 754-772. PubMed id: 19152799 DOI: 10.1016/j.jmb.2008.12.074

Date:

15-Sep-08 Release date: 24-Feb-09

Protein chain

B6ETQ5  (B6ETQ5_STRPY) -  C5a peptidase (Fragment) from Streptococcus pyogenes

Seq: 1002 a.a.

Struc: 936 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.21.110 - C5a peptidase.

DOI no: 10.1016/j.jmb.2008.12.074

J Mol Biol 386:754-772 (2009)

PubMed id: 19152799

Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9-A Crystal Structure of the Active Form of ScpA.

T.F.Kagawa, M.R.O'Connell, P.Mouat, M.Paoli, P.W.O'Toole, J.C.Cooney.

ABSTRACT

The crystal structure of an active form of ScpA has been solved to 1.9 A resolution. ScpA is a multidomain cell-envelope subtilase from Streptococcus pyogenes that cleaves complement component C5a. The catalytic triad of ScpA is geometrically consistent with other subtilases, clearly demonstrating that the additional activation mechanism proposed for the Streptococcus agalactiae homologue (ScpB) is not required for ScpA. The ScpA structure revealed that access to the catalytic site is restricted by variable regions in the catalytic domain (vr7, vr9, and vr11) and by the presence of the inserted protease-associated (PA) domain and the second fibronectin type III domains (Fn2). Modeling of the ScpA-C5a complex indicates that the substrate binds with carboxyl-terminal residues (65-74) extended through the active site and core residues (1-64), forming exosite-type interactions with the Fn2 domain. This is reminiscent of the two-site mechanism proposed for C5a binding to its receptor. In the nonprime region of the active site, interactions with the substrate backbone are predicted to be more similar to those observed in kexins, involving a single beta-strand in the peptidase. However, in contrast to kexins, there would be diminished emphasis on side-chain interactions, with little charged character in the S3-S1 and S6-S4 subsites occupied by the side chains of residues in vr7 and vr9. Substrate binding is anticipated to be dominated by ionic interactions in two distinct regions of ScpA. On the prime side of the active site, salt bridges are predicted between P1', P2', and P7' residues, and residues in the catalytic and PA domains. Remote to the active site, a larger number of ionic interactions between residues in the C5a core and the Fn2 domain are observed in the model. Thus, both PA and Fn2 domains are expected to play significant roles in substrate recognition.

Selected figure(s)

Figure 7.
Fig. 7. ScpA and its substrate C5a have complementary electrostatic surfaces. (a) Cartoon rendering of C5a NMR structure (PDB code 1KJS^38). Core helices are labeled I–IV, in order, from the N-terminus to the C-terminus. The three disulfide bonds (yellow) and the side chains of H67 (P1) and K68 (P1′) are shown as stick models. The location of the scissile bond is indicated by an arrow. Dimensions of C5a are shown with the smallest dimension (21 Å) perpendicular to the plane of the page. (b and c) Electrostatic potential surfaces of ScpA and C5a, respectively. The isopotential surfaces are contoured at − 1 kT/e (red) and + 1 kT/e (blue). For ScpA, sites 1–3 refer to the major electronegative patches on the ScpA surface. The position of the Fn2 ‘platform’ is indicated by a yellow oval, with the length across the platform (defined as the distance between A264 and G827) indicated. The yellow arrowhead shows the entrance to cleft B (approximate locations of clefts A and B are indicated). The orientation of C5a in (c) is the same as in (a). ScpA and C5a are not drawn on equivalent scales in these panels.

Figure 8.
Fig. 8. Model of the complex of ScpA and its substrate C5a. (a) Stereo diagram of the ScpA–C5a model. ScpA is shown as a solvent-accessible surface rendering, colored as in Fig. 1c. C5a is shown in orange, with the core residues shown with solvent-accessible surfaces and with the tail residues shown as a space-filling model. Substrate–enzyme interactions are shown as stereo diagrams of the nonprime region (b) and prime region (c), and in an ‘open book’ representation for interactions with the Fn2 domain (d). In (b), (c), and (d), ScpA carbon atoms of the residues of vr5, vr7, vr9, and vr11 in the Cat domain are shown as in Fig. 3. Carbon atoms in the side chains of the active-site residues are shown in green. Residues in the PA domain are shown in blue. The position of the scissile bond is indicated with a white triangle. Pertinent ionic and H-bond interactions are indicated by black and yellow dashed lines, respectively. For the Fn2 domain, residues in the four inserted regions are shown as in Fig. 4a. In (d), groups involved in ScpA–substrate interactions are indicated, with the side chains of salt-bridged residues shown in red (acidic) and blue (basic), and with the aromatic and aliphatic side chains shown in green. Main-chain carbonyl and side chains involved in nonionic hydrogen bonding interactions are shown in purple.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 386, 754-772) copyright 2009.

Figures were selected by an automated process.