1ORW

Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with a Peptidomimetic Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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This is version 2.0 of the entry. See complete history


Literature

The Crystal Structure of Dipeptidyl Peptidase IV (CD26) Reveals its Functional Regulation and Enzymatic Mechanism

Engel, M.Hoffmann, T.Wagner, L.Wermann, M.Heiser, U.Kiefersauer, R.Huber, R.Bode, W.Demuth, H.U.Brandstetter, H.

(2003) Proc Natl Acad Sci U S A 100: 5063-5068

  • DOI: https://doi.org/10.1073/pnas.0230620100
  • Primary Citation of Related Structures:  
    1ORV, 1ORW

  • PubMed Abstract: 

    The membrane-bound glycoprotein dipeptidyl peptidase IV (DP IV, CD26) is a unique multifunctional protein, acting as receptor, binding and proteolytic molecule. We have determined the sequence and 1.8 A crystal structure of native DP IV prepared from porcine kidney. The crystal structure reveals a 2-2-2 symmetric tetrameric assembly which depends on the natively glycosylated beta-propeller blade IV. The crystal structure indicates that tetramerization of DP IV is a key mechanism to regulate its interaction with other components. Each subunit comprises two structural domains, the N-terminal eight-bladed beta-propeller with open Velcro topology and the C-terminal alpha/beta-hydrolase domain. Analogy with the structurally related POP and tricorn protease suggests that substrates access the buried active site through the beta-propeller tunnel while products leave the active site through a separate side exit. A dipeptide mimicking inhibitor complexed to the active site discloses key determinants for substrate recognition, including a Glu-Glu motif that distinguishes DP IV as an aminopeptidase and an oxyanion trap that binds and activates the P(2)-carbonyl oxygen necessary for efficient postproline cleavage. We discuss active and nonactive site-directed inhibition strategies of this pharmaceutical target protein.


  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abt. Strukturforschung, D-82152 Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dipeptidyl peptidase IV
A, B, C, D
728Sus scrofaMutation(s): 0 
EC: 3.4.14.5
UniProt
Find proteins for P22411 (Sus scrofa)
Explore P22411 
Go to UniProtKB:  P22411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22411
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, H, I, K
E, F, H, I, K, L, M
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, J
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHI
Query on PHI

Download Ideal Coordinates CCD File 
HA [auth C],
MA [auth D],
S [auth A],
Z [auth B]
IODO-PHENYLALANINE
C9 H10 I N O2
PZNQZSRPDOEBMS-QMMMGPOBSA-N
NAG
Query on NAG

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BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
JA [auth D],
KA [auth D],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
P2Y
Query on P2Y

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AA [auth B],
IA [auth C],
NA [auth D],
T [auth A]
(2S)-PYRROLIDIN-2-YLMETHYLAMINE
C5 H12 N2
AUKXFNABVHIUAC-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
GA [auth C],
LA [auth D],
R [auth A],
Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.97α = 112.65
b = 117.71β = 94.81
c = 133.56γ = 91.17
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MAINphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary