PDBsum entry 3ch2

Hydrolase

PDB id: 3ch2

Contents

Protein chain

256 a.a. *

Metals

_CA

Waters ×230

* Residue conservation analysis

PDB id:

3ch2

Name:

Hydrolase

Title:

Crystal structure analysis of sera5e from plasmodium falciparum

Structure:

Serine-repeat antigen protein. Chain: x. Fragment: putative serine protease domain, unp residues 564-828. Synonym: p126, 111 kda antigen, sera5. Engineered: yes

Source:

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. Gene: sera5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.168 R-free: 0.198

Authors:

B.J.Smith,R.L.Malby,P.M.Colman,O.B.Clarke

Key ref:

A.N.Hodder et al. (2009). Structural insights into the protease-like antigen Plasmodium falciparum SERA5 and its noncanonical active-site serine. J Mol Biol, 392, 154-165. PubMed id: 19591843 DOI: 10.1016/j.jmb.2009.07.007

Date:

07-Mar-08 Release date: 25-Mar-08

Protein chain

Q9TY95  (SERA_PLAF7) -  Serine-repeat antigen protein 5 from Plasmodium falciparum (isolate 3D7)

Seq: 997 a.a.

Struc: 256 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.22.- - ?????

DOI no: 10.1016/j.jmb.2009.07.007

J Mol Biol 392:154-165 (2009)

PubMed id: 19591843

Structural insights into the protease-like antigen Plasmodium falciparum SERA5 and its noncanonical active-site serine.

A.N.Hodder, R.L.Malby, O.B.Clarke, W.D.Fairlie, P.M.Colman, B.S.Crabb, B.J.Smith.

ABSTRACT

The sera genes of the malaria-causing parasite Plasmodium encode a family of unique proteins that are maximally expressed at the time of egress of parasites from infected red blood cells. These multi-domain proteins are unique, containing a central papain-like cysteine-protease fragment enclosed between the disulfide-linked N- and C-terminal domains. However, the central fragment of several members of this family, including serine repeat antigen 5 (SERA5), contains a serine (S596) in place of the active-site cysteine. Here we report the crystal structure of the central protease-like domain of Plasmodium falciparum SERA5, revealing a number of anomalies in addition to the putative nucleophilic serine: (1) the structure of the putative active site is not conducive to binding substrate in the canonical cysteine-protease manner; (2) the side chain of D594 restricts access of substrate to the putative active site; and (3) the S(2) specificity pocket is occupied by the side chain of Y735, reducing this site to a small depression on the protein surface. Attempts to determine the structure in complex with known inhibitors were not successful. Thus, despite having revealed its structure, the function of the catalytic domain of SERA5 remains an enigma.

Selected figure(s)

Figure 1.
Fig. 1. Sequence alignment of cathepsin L and SERA5E. (a) Structural alignment^29 of SERA5E with the enzyme domain of cathepsin L (CatL; PDB 1mhw). Secondary-structure elements (helices and strands, cylinders and arrows, respectively) in SERA5E are indicated. Lowercase font refers to structurally unaligned regions. (b) Secondary-structure topology of SERA5E, showing disulfide bonding between cysteine residues; disulfide bonds unique to SERA5E are asterisked (1–2* between C567 and C572, 3–5* between C581 and C610). Black circles indicate the relative disposition of the triad of catalytic residues S596, H762, and N787.

Figure 2.
Fig. 2. Structural comparison of SERA5E and cathepsin L. (a) Cartoon diagram of SERA5E. The N-terminal domain is to the left and the C-terminal domain to the right of the central catalytic cleft. The side-chain atoms of the catalytic triad, S596, H762, and N787, are shown along with those from residues that line the substrate-binding cleft, Q590, D594, D637, E638, S641, M643, K701, Y703, A705, E707, R710, Y735, S816, and V818. The residues connecting N691 to D699 in SERA5E are disordered in structures 1 and 2. (b) Cartoon diagram of cathepsin L. The side-chain atoms of the catalytic triad in cathepsin L, C25, H163, and N187 are highlighted, along with the side-chain atoms of A135, composing the S[2] pocket. (c) Structural comparison of the substrate-binding sites. The peptide backbone atoms of SERA5E G639–S641 and cathepsin L G67–L69 are shown. The peptide plane of G639 in structure 1 and structure 2 of SERA5E is rotated vert, similar 90° compared to the orientation of the equivalent residue in cathepsin L, whereas in structure 3, there is a rotation of vert, similar 45° of this and the proceeding peptide plane (S640). The loop in the N-terminal domain leading to the strand responsible for orienting substrates [C627–G639 and C56–G67 in SERA5E (tan) and cathepsin L (cyan), respectively] is highlighted—this loop adopts a different path in SERA5E compared to that in cathepsin L. The disulfide bond at the C-terminal end of this loop is indicated. The side chains of the catalytic-triad residues in SERA5E (S596, H762, N787) are found in identical orientations and positions in cathepsin L (C25, H163, N187). The S[2] pocket in cathepsin L, formed in part by A135, is occupied by Y735 in SERA5E.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 392, 154-165) copyright 2009.

Figures were selected by the author.