6EOP

DPP8 - SLRFLYEG, space group 20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer.

Ross, B.Krapp, S.Augustin, M.Kierfersauer, R.Arciniega, M.Geiss-Friedlander, R.Huber, R.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E1437-E1445

  • DOI: 10.1073/pnas.1717565115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterize ...

    Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.


    Organizational Affiliation

    Max Planck Institut für Biochemie, D-82152 Martinsried, Germany; ross@biochem.mpg.de huber@biochem.mpg.de.,Abteilung für Molekularbiologie, Universitätsmedizin Göttingen, D-37073 Göttingen, Germany.,Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, D-45117 Essen, Germany.,Proteros Biostructures GmbH, D-82152 Martinsried, Germany.,Fakultät für Chemie, Technische Universität München, D-85747 Garching, Germany.,Department of Biochemistry and Structural Biology, Institute of Cellular Physiology, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 8
A, B, C
898Homo sapiensMutation(s): 0 
Gene Names: DPP8 (DPRP1)
EC: 3.4.14.5
Find proteins for Q6V1X1 (Homo sapiens)
Go to Gene View: DPP8
Go to UniProtKB:  Q6V1X1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
D, E, F
8Homo sapiensMutation(s): 0 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

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Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
F15
Query on F15

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Download CCD File 
D, E, F
PENTADECANOIC ACID
C15 H30 O2
WQEPLUUGTLDZJY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B, C
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 162.830α = 90.00
b = 246.371β = 90.00
c = 261.191γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-10-10 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Ross, B.R., Huber, R.

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references
  • Version 1.2: 2018-02-28
    Type: Database references