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PDBsum entry 1d5g

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protein Protein-protein interface(s) links
Hydrolase PDB id
1d5g
Jmol
Contents
Protein chains
96 a.a. *
15 a.a. *
* Residue conservation analysis
PDB id:
1d5g
Name: Hydrolase
Title: Solution structure of the pdz2 domain from human phosphatase hptp1e complexed with a peptide
Structure: Human phosphatase hptp1e. Chain: a. Fragment: pdz2 domain. Engineered: yes. Peptide fadseadeneqvsav. Chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized.
NMR struc: 20 models
Authors: G.Kozlov,K.Gehring,I.Ekiel
Key ref:
G.Kozlov et al. (2002). Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions. J Mol Biol, 320, 813-820. PubMed id: 12095257 DOI: 10.1016/S0022-2836(02)00544-2
Date:
07-Oct-99     Release date:   24-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q12923  (PTN13_HUMAN) -  Tyrosine-protein phosphatase non-receptor type 13
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2485 a.a.
96 a.a.
Protein chain
No UniProt id for this chain
Struc: 15 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.3.1.3.48  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00544-2 J Mol Biol 320:813-820 (2002)
PubMed id: 12095257  
 
 
Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions.
G.Kozlov, D.Banville, K.Gehring, I.Ekiel.
 
  ABSTRACT  
 
The solution structure of the second PDZ domain from human phosphatase hPTP1E in complex with a C-terminal peptide from the guanine nucleotide exchange factor RA-GEF-2 has been determined using 2D and 3D heteronuclear NMR experiments. Compared to previously solved structures, the hPTP1E complex shows an enlarged interaction surface with the C terminus of the bound peptide. Novel contacts were found between the long structured beta2/beta3 loop of the PDZ domain and the sixth amino acid residue from the C terminus of the peptide. This work underlines the importance of the beta2/beta3 loop for ligand selection by PDZ domains.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Stereo view backbone overlay of the 20 lowest-energy NMR structures of PDZ2 domain from human phosphatase hPTP1E complexed with a peptide. (b) Ribbon representation of the average PDZ2/peptide complex structure generated with MOLSCRIPT[40] and Raster3D. [41] The b-strands of PDZ2 domain are labeled b1-b6 and the a-helices are labeled a1 and a2. The b-strand of the peptide is labeled b0.
Figure 2.
Figure 2. Stereo view of the binding site. The peptide is shown in yellow, the a2 helix of PDZ2 domain is in red. For clarity, side-chains of only selected residues are shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 813-820) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21376703 J.H.Lee, H.Park, S.J.Park, H.J.Kim, and S.H.Eom (2011).
The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands.
  Biochem Biophys Res Commun, 407, 207-212.
PDB codes: 3qjm 3qjn
20047332 R.C.Tyler, F.C.Peterson, and B.F.Volkman (2010).
Distal interactions within the par3-VE-cadherin complex.
  Biochemistry, 49, 951-957.
PDB code: 2koh
19679084 A.del Sol, C.J.Tsai, B.Ma, and R.Nussinov (2009).
The origin of allosteric functional modulation: multiple pre-existing pathways.
  Structure, 17, 1042-1050.  
18618698 Y.Kong, and M.Karplus (2009).
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.
  Proteins, 74, 145-154.  
17473018 Q.Chen, X.Niu, Y.Xu, J.Wu, and Y.Shi (2007).
Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex.
  Protein Sci, 16, 1053-1062.
PDB code: 2ain
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
  16796391 A.Piserchio, M.Spaller, and D.F.Mierke (2006).
Targeting the PDZ domains of molecular scaffolds of transmembrane ion channels.
  AAPS J, 8, E396-E401.  
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
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.  
15684424 H.Zhou, Y.Xu, Y.Yang, A.Huang, J.Wu, and Y.Shi (2005).
Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr.
  J Biol Chem, 280, 13841-13847.
PDB code: 1t2m
15978037 L.C.van den Berk, E.Landi, E.Harmsen, L.Dente, and W.J.Hendriks (2005).
Redox-regulated affinity of the third PDZ domain in the phosphotyrosine phosphatase PTP-BL for cysteine-containing target peptides.
  FEBS J, 272, 3306-3316.  
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.  
16049001 S.Gianni, A.Engström, M.Larsson, N.Calosci, F.Malatesta, L.Eklund, C.C.Ngang, C.Travaglini-Allocatelli, and P.Jemth (2005).
The kinetics of PDZ domain-ligand interactions and implications for the binding mechanism.
  J Biol Chem, 280, 34805-34812.  
15123241 A.Piserchio, G.D.Salinas, T.Li, J.Marshall, M.R.Spaller, and D.F.Mierke (2004).
Targeting specific PDZ domains of PSD-95; structural basis for enhanced affinity and enzymatic stability of a cyclic peptide.
  Chem Biol, 11, 469-473.
PDB code: 1rgr
15123239 P.Boisguerin, R.Leben, B.Ay, G.Radziwill, K.Moelling, L.Dong, and R.Volkmer-Engert (2004).
An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies.
  Chem Biol, 11, 449-459.  
14725761 T.Walma, J.Aelen, S.B.Nabuurs, M.Oostendorp, L.van den Berk, W.Hendriks, and G.W.Vuister (2004).
A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL.
  Structure, 12, 11-20.
PDB code: 1ozi
12842047 B.S.Kang, D.R.Cooper, Y.Devedjiev, U.Derewenda, and Z.S.Derewenda (2003).
Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm.
  Structure, 11, 845-853.
PDB codes: 1nte 1obx 1oby 1obz
12444095 G.Birrane, J.Chung, and J.A.Ladias (2003).
Novel mode of ligand recognition by the Erbin PDZ domain.
  J Biol Chem, 278, 1399-1402.
PDB codes: 1mfg 1mfl
14653806 K.S.Erdmann (2003).
The protein tyrosine phosphatase PTP-Basophil/Basophil-like. Interacting proteins and molecular functions.
  Eur J Biochem, 270, 4789-4798.  
12446668 N.J.Skelton, M.F.Koehler, K.Zobel, W.L.Wong, S.Yeh, M.T.Pisabarro, J.P.Yin, L.A.Lasky, and S.S.Sidhu (2003).
Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain.
  J Biol Chem, 278, 7645-7654.
PDB code: 1n7t
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.  
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.