› 5yp2

X-ray diffraction
2.13Å resolution

Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24

Released:
DOI: 10.2210/pdb5yp2/pdb
PDB entry 5yp2 coloured by chain, front view.
PDB entry 5yp2 coloured by chain, side view.
PDB entry 5yp2 coloured by chain, top view.
Source organism: Pseudoxanthomonas mexicana
Primary publication:
Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Roppongi S, Suzuki Y, Tateoka C, Fujimoto M, Morisawa S, Iizuka I, Nakamura A, Honma N, Shida Y, Ogasawara W, Tanaka N, Sakamoto Y, Nonaka T
Sci Rep 8 2714 (2018)
PMID: 29426867

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179587 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidyl aminopeptidase 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 745 amino acids
Theoretical weight: 82.38 KDa
Source organism: Pseudoxanthomonas mexicana
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q6F3I7 (Residues: 1-745; Coverage: 100%)
Gene name: dap4
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand 8YC 2 x 8YC
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P212121
Unit cell:
a: 59.88Å b: 120.22Å c: 231.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.226
Expression system: Escherichia coli K-12

Quick links

Citations

1 review citation

Discovery of Food-Derived Dipeptidyl Peptidase IV Inhibitory Peptides: A Review.
Liu et al. (2019)
6 other articles

1 mention without citation

Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Roppongi et al. (2018)