spacer
spacer

PDBsum entry 1gm1

Go to PDB code: 
protein links
Hydrolase PDB id
1gm1
Jmol
Contents
Protein chain
94 a.a. *
* Residue conservation analysis
PDB id:
1gm1
Name: Hydrolase
Title: Second pdz domain (pdz2) of ptp-bl
Structure: Protein tyrosine phosphatase. Chain: a. Fragment: pdz2. Synonym: nonreceptor-type, 13, protein-tyrosine phosphatase rip, phosphoprotein phosphatase, protein-tyrosine-phosphatase, phosphotyrosine phosphatase, ptpase, ptp36, bas-like. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3.
NMR struc: 35 models
Authors: T.Walma,M.Tessari,J.Aelen,J.Schepens,W.Hendriks,G.W.Vuister
Key ref:
T.Walma et al. (2002). Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL. J Mol Biol, 316, 1101-1110. PubMed id: 11884147 DOI: 10.1006/jmbi.2002.5402
Date:
06-Sep-01     Release date:   08-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q64512  (PTN13_MOUSE) -  Tyrosine-protein phosphatase non-receptor type 13
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2453 a.a.
94 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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: 10.1006/jmbi.2002.5402 J Mol Biol 316:1101-1110 (2002)
PubMed id: 11884147  
 
 
Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL.
T.Walma, C.A.Spronk, M.Tessari, J.Aelen, J.Schepens, W.Hendriks, G.W.Vuister.
 
  ABSTRACT  
 
The PDZ domains of the protein tyrosine phosphatase PTP-BL mediate interactions by binding to specific amino acid sequences in target proteins. The solution structure of the second PDZ domain of PTP-BL, PDZ2, displays a compact fold with six beta strands and two alpha-helices. A unique feature of this domain compared to the canonical PDZ fold is an extended flexible loop at the base of the binding pocket, termed L1, that folds back onto the protein backbone, a feature that is shared by both the murine and human orthologues. The structure of PDZ2 differs significantly from the orthologous human structure. A comparison of structural quality indicators clearly demonstrates that the PDZ2 ensemble is statistically more reasonable than that of the human orthologue. The analysis of (15)N relaxation data for PDZ2 shows a normal pattern, with more rigid secondary structures and more flexible loop structures. Close to the binding pocket, Leu85 and Thr88 display greater mobility when compared to surrounding residues. Peptide binding studies demonstrated a lack of interaction between murine PDZ2 and the C terminus of the murine Fas/CD95 receptor, suggesting that the Fas/CD95 receptor is not an in vivo target for PDZ2. In addition, PDZ2 specifically binds the C termini of both human Fas/CD95 receptor and the RIL protein, despite RIL containing a non-canonical PDZ-interacting sequence of E-x-V. A model of PDZ2 with the RIL peptide reveals that the PDZ2 binding pocket is able to accommodate the bulkier side-chain of glutamic acid while maintaining crucial protein to peptide hydrogen bond interactions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) Structural ensemble of 35 PDZ2 structures (stereo diagram). (b) Structural superposition of PDZ2 (blue) with PDZ domains from PTP-Bas (green), DlgA (yellow), CASK (magenta) and syntrophin (red). Detail of the flexible loop region (circle): PDZ2 and its human orthologue possess an extended loop L1. (c) Sequence alignment corresponding to the structural superposition in (b). Secondary structures of PDZ2 are indicated by blue (b-strand) and red (a-helix) color-coding. Regions that are structurally conserved with respect to PDZ2 (as calculated by WHAT-IF[24]) are shaded gray. Boxes surround regions that are structurally conserved across all three class representatives and contain residues that were used in RMSD comparisons.
Figure 3.
Figure 3. PDZ2 color-coded according to changes in backbone hydrogen and nitrogen chemical shift upon titration of (a) human Fas receptor, (b) mouse Fas receptor, and (c) RIL C-terminal peptides. (d) Surface representation of (c) with RIL peptide (gold) modelled into the binding pocket. According to the given scale, the blue-to-red gradient of the surface coloring represents smaller to larger changes in chemical shift. Grey coloring indicates that no data was available. Broken green lines indicate putative hydrogen bonds based on typical distance and angles constraints.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 1101-1110) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21422294 B.Balana, I.Maslennikov, W.Kwiatkowski, K.M.Stern, L.Bahima, S.Choe, and P.A.Slesinger (2011).
Mechanism underlying selective regulation of G protein-gated inwardly rectifying potassium channels by the psychostimulant-sensitive sorting nexin 27.
  Proc Natl Acad Sci U S A, 108, 5831-5836.
PDB codes: 3qdo 3qe1 3qgl
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
  20052683 B.K.Ho, and D.A.Agard (2010).
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.
  Protein Sci, 19, 398-411.  
19933699 F.Giansanti, L.Di Leandro, I.Koutris, G.Pitari, M.S.Fabbrini, A.Lombardi, D.J.Flavell, S.U.Flavell, S.Gianni, and R.Ippoliti (2010).
Engineering a switchable toxin: the potential use of PDZ domains in the expression, targeting and activation of modified saporin variants.
  Protein Eng Des Sel, 23, 61-68.  
20563762 G.Kock, M.Dicks, R.Heumann, K.S.Erdmann, and R.Stoll (2010).
Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL.
  Biomol NMR Assign, 4, 199-202.  
19289055 A.Sicorello, S.Torrassa, G.Soldi, S.Gianni, C.Travaglini-Allocatelli, N.Taddei, A.Relini, and F.Chiti (2009).
Agitation and high ionic strength induce amyloidogenesis of a folded PDZ domain in native conditions.
  Biophys J, 96, 2289-2298.  
18618698 Y.Kong, and M.Karplus (2009).
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.
  Proteins, 74, 145-154.  
19033470 N.Calosci, C.N.Chi, B.Richter, C.Camilloni, A.Engström, L.Eklund, C.Travaglini-Allocatelli, S.Gianni, M.Vendruscolo, and P.Jemth (2008).
Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins.
  Proc Natl Acad Sci U S A, 105, 19241-19246.  
16132821 A.E.Duquesne, M.Ruijter, J.Brouwer, J.W.Drijfhout, S.B.Nabuurs, C.A.Spronk, G.W.Vuister, M.Ubbink, and G.W.Canters (2005).
Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase.
  J Biomol NMR, 32, 209-218.
PDB code: 1y7n
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.  
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.  
15023337 F.C.Peterson, R.R.Penkert, B.F.Volkman, and K.E.Prehoda (2004).
Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition.
  Mol Cell, 13, 665-676.
PDB codes: 1ry4 1rzx
15663004 L.C.van den Berk, M.A.van Ham, M.M.te Lindert, T.Walma, J.Aelen, G.W.Vuister, and W.J.Hendriks (2004).
The interaction of PTP-BL PDZ domains with RIL: an enigmatic role for the RIL LIM domain.
  Mol Biol Rep, 31, 203-215.  
15461663 R.G.Chirivi, G.Dilaver, R.van de Vorstenbosch, B.Wanschers, J.Schepens, H.Croes, J.Fransen, and W.Hendriks (2004).
Characterization of multiple transcripts and isoforms derived from the mouse protein tyrosine phosphatase gene Ptprr.
  Genes Cells, 9, 919-933.  
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.  
12724420 V.N.Ivanov, P.Lopez Bergami, G.Maulit, T.A.Sato, D.Sassoon, and Z.Ronai (2003).
FAP-1 association with Fas (Apo-1) inhibits Fas expression on the cell surface.
  Mol Cell Biol, 23, 3623-3635.  
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.