PDBsum entry 6vgo

Hydrolase

PDB id: 6vgo

Contents

Protein chain

350 a.a.

Waters ×220

PDB id:

6vgo

Name:

Hydrolase

Title:

Crystal structure of human dipeptidase 3

Structure:

Dipeptidase 3. Chain: a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dpep3, unq834/pro1772. Expressed in: cricetulus griseus. Expression_system_taxid: 10029

Resolution:

1.82Å R-factor: 0.187 R-free: 0.214

Authors:

K.Hayashi,K.L.Longenecker,S.Vivona

Key ref:

K.Hayashi et al. (2020). Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity. J Struct Biol, 211, 107512. PubMed id: 32325220 DOI: 10.1016/j.jsb.2020.107512

Date:

08-Jan-20 Release date: 13-May-20

Protein chain

Q9H4B8  (DPEP3_HUMAN) -  Dipeptidase 3 from Homo sapiens

Seq: 488 a.a.

Struc: 350 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.13.19 - membrane dipeptidase.
• Reaction: an L-aminoacyl-L-amino acid + H2O = 2 an L-alpha-amino acid
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.jsb.2020.107512

J Struct Biol 211:107512 (2020)

PubMed id: 32325220

Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity.

K.Hayashi, K.L.Longenecker, P.Koenig, A.Prashar, J.Hampl, V.Stoll, S.Vivona.

ABSTRACT

Dipeptidase 3 (DPEP3) is one of three glycosylphosphatidylinositol-anchored metallopeptidases potentially involved in the hydrolytic metabolism of dipeptides. While its exact biological function is not clear, DPEP3 expression is normally limited to testis, but can be elevated in ovarian cancer. Antibody drug conjugates targeting DPEP3 have shown efficacy in preclinical models with a pyrrolobenzodiazepine conjugate, SC-003, dosed in a phase I clinical trial (NCT02539719). Here we reveal the novel atomic structure of DPEP3 alone and in complex with the SC-003 Fab fragment at 1.8 and 2.8 Å, respectively. The structure of DPEP3/SC-003 Fab complex reveals an eighteen-residue epitope across the DPEP3 dimerization interface distinct from the enzymatic active site. DPEP1 and DPEP3 extracellular domains share a conserved, dimeric TIM (β/α)8-barrel fold, consistent with 49% sequence identity. However, DPEP3 diverges from DPEP1 and DPEP2 in key positions of its active site: a histidine to tyrosine variation at position 269 reduces affinity for the β zinc and may cause substrate steric hindrance, whereas an aspartate to asparagine change at position 359 abolishes activation of the nucleophilic water/hydroxide, resulting in no in vitro activity against a variety of dipeptides and biological substrates (imipenem, leukotriene D4 and cystinyl-bis-glycine). Hence DPEP3, unlike DPEP1 and DPEP2, may require an activating co-factor in vivo or may remain an inactive, degenerate enzyme. This report sheds light on the structural discriminants between active and inactive membrane dipeptidases and provides a benchmark to characterize current and future DPEP3-targeted therapeutic approaches.