2BGN

HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structures of HIV-1 Tat-Derived Nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) Bound to the Active Site of Dipeptidyl-Peptidase Iv (Cd26)

Weihofen, W.A.Liu, J.Reutter, W.Saenger, W.Fan, H.

(2005) J Biol Chem 280: 14911

  • DOI: 10.1074/jbc.M413400200
  • Primary Citation of Related Structures:  
    2BGN, 2BGR

  • PubMed Abstract: 
  • CD26 or dipeptidyl-peptidase IV (DPPIV) is engaged in immune functions by co-stimulatory effects on activation and proliferation of T lymphocytes, binding to adenosine deaminase, and regulation of various chemokines and cytokines. DPPIV peptidase activity is inhibited by both Tat protein from human immunodeficiency virus (HIV)-1 and its N-terminal nonapeptide Tat-(1-9) with amino acid sequence MDPVDPNIE, suggesting that DPPIV mediates immunosuppressive effects of Tat protein ...

    CD26 or dipeptidyl-peptidase IV (DPPIV) is engaged in immune functions by co-stimulatory effects on activation and proliferation of T lymphocytes, binding to adenosine deaminase, and regulation of various chemokines and cytokines. DPPIV peptidase activity is inhibited by both Tat protein from human immunodeficiency virus (HIV)-1 and its N-terminal nonapeptide Tat-(1-9) with amino acid sequence MDPVDPNIE, suggesting that DPPIV mediates immunosuppressive effects of Tat protein. The 2.0- and 3.15-A resolution crystal structures of the binary complex between human DPPIV and nonapeptide Tat-(1-9) and the ternary complex between the variant MWPVDPNIE, called Trp(2)-Tat-(1-9), and DPPIV bound to adenosine deaminase show that Tat-(1-9) and Trp(2)-Tat-(1-9) are located in the active site of DPPIV. The interaction pattern of DPPIV with Trp(2)-Tat-(1-9) is tighter than that with Tat-(1-9), in agreement with inhibition constants (K(i)) of 2 x 10(-6) and 250 x 10(-6) m, respectively. Both peptides cannot be cleaved by DPPIV because the binding pockets of the N-terminal 2 residues are interchanged compared with natural substrates: the N-terminal methionine occupies the hydrophobic S1 pocket of DPPIV that normally accounts for substrate specificity by binding the penultimate residue. Because the N-terminal sequence of the thromboxane A2 receptor resembles the Trp(2)-Tat-(1-9) peptide, a possible interaction with DPPIV is postulated.


    Organizational Affiliation

    Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE IVA, B, C, D728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
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Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ADENOSINE DEAMINASEE, F, G, H363Bos taurusMutation(s): 3 
Gene Names: ADA
EC: 3.5.4.4
Find proteins for P56658 (Bos taurus)
Explore P56658 
Go to UniProtKB:  P56658
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TAT PROTEINI [auth W], J [auth X], K [auth Y], L [auth Z]9Human immunodeficiency virus 1Mutation(s): 1 
Find proteins for P12506 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth I], V [auth R]3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b], DA [auth d], N [auth J], O [auth K], Q [auth M], S [auth O], U [auth Q], W [auth S]
BA [auth b], DA [auth d], N [auth J], O [auth K], Q [auth M], S [auth O], U [auth Q], W [auth S], X [auth T], Z [auth V]
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c], P [auth L], T [auth P], Y [auth U]4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a], R [auth N]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth A] , FA [auth A] , GA [auth A] , HA [auth B] , IA [auth B] , JA [auth B] , KA [auth B] , LA [auth C] , 
EA [auth A],  FA [auth A],  GA [auth A],  HA [auth B],  IA [auth B],  JA [auth B],  KA [auth B],  LA [auth C],  MA [auth C],  NA [auth C],  OA [auth D],  PA [auth D],  QA [auth D],  RA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
SA [auth E], TA [auth F], UA [auth G], VA [auth H]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.945α = 90
b = 170.273β = 100.93
c = 239.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary