PDBsum entry 1pfq

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
Protein chain
728 a.a. *
NAG ×4
Waters ×472
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of human apo dipeptidyl peptidase iv / cd2
Structure: Dipeptidyl peptidase iv soluble form. Chain: a, b. Synonym: dpp iv, t-cell activation antigen cd26, tp103, ade deaminase complexing protein-2, adabp. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: dpp4 or adcp2 or cd26. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Biol. unit: Dimer (from PQS)
1.90Å     R-factor:   0.256     R-free:   0.298
Authors: C.Oefner,A.D'Arcy,A.Mac Sweeney,S.Pierau,R.Gardiner,G.E.Dale
Key ref:
C.Oefner et al. (2003). High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine. Acta Crystallogr D Biol Crystallogr, 59, 1206-1212. PubMed id: 12832764 DOI: 10.1107/S0907444903010059
27-May-03     Release date:   01-Jul-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P27487  (DPP4_HUMAN) -  Dipeptidyl peptidase 4
766 a.a.
728 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dipeptidyl-peptidase Iv.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of an N-terminal dipeptide, Xaa-Xbb-|-Xcc, from a polypeptide, preferentially when Xbb is Pro, provided Xcc is neither Pro nor hydroxyproline.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   16 terms 
  Biological process     cell adhesion   9 terms 
  Biochemical function     protein binding     11 terms  


DOI no: 10.1107/S0907444903010059 Acta Crystallogr D Biol Crystallogr 59:1206-1212 (2003)
PubMed id: 12832764  
High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine.
C.Oefner, A.D'Arcy, A.Mac Sweeney, S.Pierau, R.Gardiner, G.E.Dale.
Dipeptidyl peptidase IV is a multifunctional type II transmembrane serine protease glycoprotein. The high-resolution crystal structure of the homodimeric human apo dipeptidyl peptidase IV has been determined at 1.9 A resolution. In addition, the structure of the binary complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine has been solved, revealing the nature of the covalent interaction with the active-site serine.
  Selected figure(s)  
Figure 2.
Figure 2 Structure of the competitive iodinated inhibitor 1-[({2-[(5-iodopyridin-2-yl)amino]-ethyl}amino)-acetyl]-2-cyano-(S)-pyrrolidine, which is a derivative of the Novartis compound NVP-DPP728.
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 1206-1212) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20536396 M.R.Pitman, R.I.Menz, and C.A.Abbott (2010).
Hydrophilic residues surrounding the S1 and S2 pockets contribute to dimerisation and catalysis in human dipeptidyl peptidase 8 (DP8).
  Biol Chem, 391, 959-972.  
20306218 S.Jang, T.Y.Chung, J.Shin, K.L.Lin, J.T.Tzen, and F.Y.Li (2010).
Docking study of the precursor peptide of mastoparan onto its putative processing enzyme, dipeptidyl peptidase IV: a revisit to molecular ticketing.
  J Comput Aided Mol Des, 24, 213-224.  
17068815 C.Rummey, and G.Metz (2007).
Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site.
  Proteins, 66, 160-171.  
17492130 H.Hiramatsu, K.Kyono, A.Yamamoto, K.Saeki, H.Shima, S.Sugiyama, K.Inaka, and R.Shimizu (2007).
Crystal structures of human dipeptidyl peptidase IV in its apo and diprotin B-complexed forms.
  Acta Biochim Biophys Sin (Shanghai), 39, 335-343.  
17884461 J.G.Robertson (2007).
Enzymes as a special class of therapeutic target: clinical drugs and modes of action.
  Curr Opin Struct Biol, 17, 674-679.  
16622600 M.Werle, and A.Bernkop-Schnürch (2006).
Strategies to improve plasma half life time of peptide and protein drugs.
  Amino Acids, 30, 351-367.  
  16511202 H.Wright, A.L.Kiss, Z.Szeltner, L.Polgár, and V.Fülöp (2005).
Crystallization and preliminary crystallographic analysis of porcine acylaminoacyl peptidase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 942-944.  
15819895 P.Rigolet, X.G.Xi, S.Rety, and J.F.Chich (2005).
The structural comparison of the bacterial PepX and human DPP-IV reveals sites for the design of inhibitors of PepX activity.
  FEBS J, 272, 2050-2059.  
15175333 J.R.Bjelke, J.Christensen, S.Branner, N.Wagtmann, C.Olsen, A.B.Kanstrup, and H.B.Rasmussen (2004).
Tyrosine 547 constitutes an essential part of the catalytic mechanism of dipeptidyl peptidase IV.
  J Biol Chem, 279, 34691-34697.
PDB codes: 1tk3 1tkr 1to7 1u8e
14718659 K.Aertgeerts, S.Ye, M.G.Tennant, M.L.Kraus, J.Rogers, B.C.Sang, R.J.Skene, D.R.Webb, and G.S.Prasad (2004).
Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation.
  Protein Sci, 13, 412-421.
PDB codes: 1r9m 1r9n
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.