PDBsum entry 3pdz

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protein links
Hydrolase PDB id
Protein chain
96 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Solution structure of the pdz2 domain from human phosphatase hptp1e
Structure: Protein (tyrosine phosphatase (ptp-bas, type 1)). Chain: a. Fragment: pdz2 domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 30 models
Authors: G.Kozlov,K.Gehring,I.Ekiel
Key ref:
G.Kozlov et al. (2000). Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor. Biochemistry, 39, 2572-2580. PubMed id: 10704206 DOI: 10.1021/bi991913c
10-May-99     Release date:   17-Mar-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q12923  (PTN13_HUMAN) -  Tyrosine-protein phosphatase non-receptor type 13
2485 a.a.
96 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain


DOI no: 10.1021/bi991913c Biochemistry 39:2572-2580 (2000)
PubMed id: 10704206  
Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor.
G.Kozlov, K.Gehring, I.Ekiel.
The solution structure of the second PDZ domain (PDZ2) from human phosphatase hPTP1E has been determined using 2D and 3D heteronuclear NMR experiments. The binding of peptides derived from the C-terminus of the Fas receptor to PDZ2 was studied via changes in backbone peptide and protein resonances. The structure is based on a total of 1387 nonredundant experimental NMR restraints including 1261 interproton distance restraints, 45 backbone hydrogen bonds, and 81 torsion angle restraints. Analysis of 30 lowest-energy structures resulted in rmsd values of 0.41 +/- 0.09 A for backbone atoms (N, Calpha, C') and 1.08 +/- 0.10 A for all heavy atoms, excluding the disordered N- and C-termini. The hPTP1E PDZ2 structure is similar to known PDZ domain structures but contains two unique structural features. In the peptide binding domain, the first glycine of the GLGF motif is replaced by a serine. This serine appears to replace a bound water observed in PDZ crystal structures that hydrogen bonds to the bound peptide's C-terminus. The hPTP1E PDZ2 structure also contains an unusually large loop following strand beta2 and proximal to the peptide binding site. This well-ordered loop folds back against the PDZ domain and contains several residues that undergo large amide chemical shift changes upon peptide binding. Direct observation of peptide resonances demonstrates that as many as six Fas peptide residues interact with the PDZ2 domain.

Literature references that cite this PDB file's key reference

  PubMed id Reference
23178454 R.Baker, S.M.Lewis, A.T.Sasaki, E.M.Wilkerson, J.W.Locasale, L.C.Cantley, B.Kuhlman, H.G.Dohlman, and S.L.Campbell (2013).
Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function.
  Nat Struct Mol Biol, 20, 46-52.  
  20842623 S.Fournane, S.Charbonnier, A.Chapelle, B.Kieffer, G.Orfanoudakis, G.Travé, M.Masson, and Y.Nominé (2011).
Surface plasmon resonance analysis of the binding of high-risk mucosal HPV E6 oncoproteins to the PDZ1 domain of the tight junction protein MAGI-1.
  J Mol Recognit, 24, 511-523.  
18618698 Y.Kong, and M.Karplus (2009).
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.
  Proteins, 74, 145-154.  
18036153 L.Peng, D.C.Popescu, N.Wang, and B.H.Shieh (2008).
Anchoring TRP to the INAD macromolecular complex requires the last 14 residues in its carboxyl terminus.
  J Neurochem, 104, 1526-1535.  
17955183 F.H.Schumann, H.Riepl, T.Maurer, W.Gronwald, K.P.Neidig, and H.R.Kalbitzer (2007).
Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions.
  J Biomol NMR, 39, 275-289.  
17962403 S.T.Runyon, Y.Zhang, B.A.Appleton, S.L.Sazinsky, P.Wu, B.Pan, C.Wiesmann, N.J.Skelton, and S.S.Sidhu (2007).
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3.
  Protein Sci, 16, 2454-2471.
PDB codes: 2joa 2p3w
17656586 Y.Zhang, B.A.Appleton, P.Wu, C.Wiesmann, and S.S.Sidhu (2007).
Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain.
  Protein Sci, 16, 1738-1750.
PDB code: 2pzd
16737969 B.A.Appleton, Y.Zhang, P.Wu, J.P.Yin, W.Hunziker, N.J.Skelton, S.S.Sidhu, and C.Wiesmann (2006).
Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity.
  J Biol Chem, 281, 22312-22320.
PDB codes: 2h2b 2h2c 2h3l 2h3m
17018532 C.N.Chi, A.Engström, S.Gianni, M.Larsson, and P.Jemth (2006).
Two conserved residues govern the salt and pH dependencies of the binding reaction of a PDZ domain.
  J Biol Chem, 281, 36811-36818.  
16737968 Y.Zhang, S.Yeh, B.A.Appleton, H.A.Held, P.J.Kausalya, D.C.Phua, W.L.Wong, L.A.Lasky, C.Wiesmann, W.Hunziker, and S.S.Sidhu (2006).
Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families.
  J Biol Chem, 281, 22299-22311.  
16258827 K.Simon, J.Xu, C.Kim, and N.R.Skrynnikov (2005).
Estimating the accuracy of protein structures using residual dipolar couplings.
  J Biomol NMR, 33, 83-93.  
15821164 P.De Los Rios, F.Cecconi, A.Pretre, G.Dietler, O.Michielin, F.Piazza, and B.Juanico (2005).
Functional dynamics of PDZ binding domains: a normal-mode analysis.
  Biophys J, 89, 14-21.  
14653806 K.S.Erdmann (2003).
The protein tyrosine phosphatase PTP-Basophil/Basophil-like. Interacting proteins and molecular functions.
  Eur J Biochem, 270, 4789-4798.  
12511555 K.Schuh, S.Uldrijan, S.Gambaryan, N.Roethlein, and L.Neyses (2003).
Interaction of the plasma membrane Ca2+ pump 4b/CI with the Ca2+/calmodulin-dependent membrane-associated kinase CASK.
  J Biol Chem, 278, 9778-9783.  
12870871 R.Papp, I.Ekiel, and A.M.English (2003).
ESI-MS and FTIR studies of the interaction between the second PDZ domain of hPTP1E and target peptides.
  Biochem Cell Biol, 81, 71-80.  
12501160 A.V.Veselovsky, Y.D.Ivanov, A.S.Ivanov, A.I.Archakov, P.Lewi, and P.Janssen (2002).
Protein-protein interactions: mechanisms and modification by drugs.
  J Mol Recognit, 15, 405-422.  
11741967 A.Y.Hung, and M.Sheng (2002).
PDZ domains: structural modules for protein complex assembly.
  J Biol Chem, 277, 5699-5702.  
12080331 J.Reina, E.Lacroix, S.D.Hobson, G.Fernandez-Ballester, V.Rybin, M.S.Schwab, L.Serrano, and C.Gonzalez (2002).
Computer-aided design of a PDZ domain to recognize new target sequences.
  Nat Struct Biol, 9, 621-627.  
11882663 S.Karthikeyan, T.Leung, and J.A.Ladias (2002).
Structural determinants of the Na+/H+ exchanger regulatory factor interaction with the beta 2 adrenergic and platelet-derived growth factor receptors.
  J Biol Chem, 277, 18973-18978.
PDB codes: 1gq4 1gq5
11320314 G.Webster, T.Leung, S.Karthikeyan, G.Birrane, and J.A.Ladias (2001).
Crystallographic characterization of the PDZ1 domain of the human Na+/H+ exchanger regulatory factor.
  Acta Crystallogr D Biol Crystallogr, 57, 714-716.  
11283303 M.Sheng, and C.Sala (2001).
PDZ domains and the organization of supramolecular complexes.
  Annu Rev Neurosci, 24, 1.  
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.