Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 173.97 kDa 
• Atom Count: 12355 
• Residue Count: 1458 
• Unique protein chains: 1

1J2E

Crystal structure of Human Dipeptidyl peptidase IV

• DOI: 10.2210/pdb1J2E/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-12-30 Released: 2003-12-30 
• Deposition Author(s): Hiramatsu, H., Kyono, K., Higashiyama, Y., Fukushima, C., Shima, H., Sugiyama, S., Inaka, K., Yamamoto, A., Shimizu, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.302 
• R-Value Work: 0.249 

Literature

The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed beta-propeller fold.

Hiramatsu, H., Kyono, K., Higashiyama, Y., Fukushima, C., Shima, H., Sugiyama, S., Inaka, K., Yamamoto, A., Shimizu, R.

(2003) Biochem Biophys Res Commun 302: 849-854

• PubMed: 12646248 
• DOI: 10.1016/s0006-291x(03)00258-4
• Primary Citation of Related Structures:  
  1J2E


• PubMed Abstract: 
  

Dipeptidyl peptidase IV (DPPIV) is a serine protease, a member of the prolyl oligopeptidase (POP) family, and has been implicated in several diseases. Therefore, the development of DPPIV selective inhibitors, which are able to control the biological function of DPPIV, is important. We determined the crystal structure of human DPPIV at 2.6A resolution. The molecule consists of a unique eight-bladed beta-propeller domain in the N-terminal region and a serine protease domain in the C-terminal region. Also, the large "cave" structure, which is thought to control the access of the substrate, is found on the side of the beta-propeller fold. Comparison of the overall amino acid sequence between human DPPIV and POP shows low homology (12.9%). In this paper, we report the structure of human DPPIV, especially focusing on a unique eight-bladed beta-propeller domain. We also discuss the way for the access of the substrate to this domain.

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Organizational Affiliation: 

Discovery Research Laboratory, Tanabe Seiyaku Co. Ltd., 3-16-86 Kashima, Yodogawa-ku, Osaka 532-8505, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase IV	A, B	740	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487 GTEx:  ENSG00000197635

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.302 
• R-Value Work: 0.249 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.04	α = 90
b = 125.92	β = 90
c = 136.84	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing
CNX	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-30 
• Released Date: 2003-12-30 
Deposition Author(s): Hiramatsu, H., Kyono, K., Higashiyama, Y., Fukushima, C., Shima, H., Sugiyama, S., Inaka, K., Yamamoto, A., Shimizu, R.

Revision History 

• Version 1.0: 2003-12-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary