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PDBsum entry 2jy7

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protein links
Protein binding PDB id
2jy7
Jmol
Contents
Protein chain
52 a.a. *
* Residue conservation analysis
PDB id:
2jy7
Name: Protein binding
Title: Nmr structure of the ubiquitin associated (uba) domain of p62 (sqstm1). Rdc refined
Structure: Ubiquitin-binding protein p62. Chain: a. Fragment: uba domain. Synonym: sequestosome-1, phosphotyrosine-independent ligand for the lck sh2 domain of 62 kda, ebi3-associated protein of 60 kda, p60, ebiap. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sqstm1, orca, osil. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: (de3).
NMR struc: 30 models
Authors: J.E.Long,R.Layfield,M.S.Searle
Key ref:
J.Long et al. (2008). Ubiquitin recognition by the ubiquitin-associated domain of p62 involves a novel conformational switch. J Biol Chem, 283, 5427-5440. PubMed id: 18083707 DOI: 10.1074/jbc.M704973200
Date:
07-Dec-07     Release date:   18-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q13501  (SQSTM_HUMAN) -  Sequestosome-1
Seq:
Struc:
440 a.a.
52 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1074/jbc.M704973200 J Biol Chem 283:5427-5440 (2008)
PubMed id: 18083707  
 
 
Ubiquitin recognition by the ubiquitin-associated domain of p62 involves a novel conformational switch.
J.Long, T.R.Gallagher, J.R.Cavey, P.W.Sheppard, S.H.Ralston, R.Layfield, M.S.Searle.
 
  ABSTRACT  
 
The p62 protein functions as a scaffold in signaling pathways that lead to activation of NF-kappaB and is an important regulator of osteoclastogenesis. Mutations affecting the receptor activator of NF-kappaB signaling axis can result in human skeletal disorders, including those identified in the C-terminal ubiquitin-associated (UBA) domain of p62 in patients with Paget disease of bone. These observations suggest that the disease may involve a common mechanism related to alterations in the ubiquitin-binding properties of p62. The structural basis for ubiquitin recognition by the UBA domain of p62 has been investigated using NMR and reveals a novel binding mechanism involving a slow exchange structural reorganization of the UBA domain to a "bound" non-canonical UBA conformation that is not significantly populated in the absence of ubiquitin. The repacking of the three-helix bundle generates a binding surface localized around the conserved Xaa-Gly-Phe-Xaa loop that appears to optimize both hydrophobic and electrostatic surface complementarity with ubiquitin. NMR titration analysis shows that the p62-UBA binds to Lys 48-linked di-ubiquitin with approximately 4-fold lower affinity than to mono-ubiquitin, suggesting preferential binding of the p62-UBA to single ubiquitin units, consistent with the apparent in vivo preference of the p62 protein for Lys 63-linked polyubiquitin chains (which adopt a more open and extended structure). The conformational switch observed on binding may represent a novel mechanism that underlies specificity in regulating signalinduced protein recognition events.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Sequence and structure of the p62 protein and its UBA domain. Schematic representation of the p62 protein and its domain structure is shown (A). The sequence of the C-terminal UBA domain is shown expanded with the numbering from the full-length protein shown (residues 387–436). The position of the conserved Met-Gly-Phe-Ser loop is underlined; Gly^410 and Gly^411 correspond to the double glycine insertion (B). The secondary structure content of the UBA domain identified in the unbound form by NMR is shown in C. NMR structure of the p62-UBA domain shows the position of mutated residues associated with Paget disease of bone (D), and a ribbon structure of the UBA domain shows the packing of core hydrophobic residues Met^401, Leu^417, Ala^427, and Ile^431 (E).
Figure 3.
FIGURE 3. Structural analysis of the p62 UBA domain and the binding surfaces of the UBA and mUb. Chemical shift perturbations are mapped to the surface of Ub on a linear scale of white to red (largest) (A), as described by the data in Fig. 2B. B, surface representation of the structure of the p62-UBA domain in the Ub-bound state showing the surface charge distribution (acidic, red, and basic, blue) and hydrophobicity (white). The structure is viewed toward the Met-Gly-Phe-Ser loop region. C, identical orientation and representation of the UBA domain of p62 showing secondary fast exchange chemical shift perturbations (red) indicative of binding interactions with mUb. These binding perturbations correlate well with the hydrophobic surface shown in B, comprising residues within loop 1 and the C terminus of helix 3. Ribbon diagram shows NMR structures of the unbound UBA domain (D) and the bound form in the presence of 6 eq of mUb (E). The structural statistics are shown in Table 1. In the unbound state the environment of the side chain of Gln^400 is defined by NOEs with residues Phe^406, Ile^424, and Leu^428 (F); in contrast, the repacking of the helices in the bound state shows that Gln^400 is close in space to Trp^412, Leu^416, and Leu^417 (G). In this conformation the side chains of Phe^406, Ile^424, and Leu^428 are more remote from Gln^400. A schematic representation of the two structures is shown to illustrate more clearly the structural reorganization and repacking of the three helices that occurs (H). The cylindrical arrows represent the orientation and polarity of the helices. H, free (blue) and bound (red) structures are shown with a common alignment of helices 1 and 2. These structures are superimposed in I, showing the different positions and orientations of helix 3 in the two forms.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 5427-5440) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21304520 C.Heinen, K.Acs, D.Hoogstraten, and N.P.Dantuma (2011).
C-terminal UBA domains protect ubiquitin receptors by preventing initiation of protein degradation.
  Nat Commun, 2, 191.  
21041446 B.E.Riley, S.E.Kaiser, T.A.Shaler, A.C.Ng, T.Hara, M.S.Hipp, K.Lage, R.J.Xavier, K.Y.Ryu, K.Taguchi, M.Yamamoto, K.Tanaka, N.Mizushima, M.Komatsu, and R.R.Kopito (2010).
Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection.
  J Cell Biol, 191, 537-552.  
20351172 F.Wu-Baer, T.Ludwig, and R.Baer (2010).
The UBXN1 protein associates with autoubiquitinated forms of the BRCA1 tumor suppressor and inhibits its enzymatic function.
  Mol Cell Biol, 30, 2787-2798.  
20167943 M.S.Willis, W.H.Townley-Tilson, E.Y.Kang, J.W.Homeister, and C.Patterson (2010).
Sent to destroy: the ubiquitin proteasome system regulates cell signaling and protein quality control in cardiovascular development and disease.
  Circ Res, 106, 463-478.  
20098416 S.Geisler, K.M.Holmström, D.Skujat, F.C.Fiesel, O.C.Rothfuss, P.J.Kahle, and W.Springer (2010).
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1.
  Nat Cell Biol, 12, 119-131.  
19722279 J.Song, J.K.Park, J.J.Lee, Y.S.Choi, K.S.Ryu, J.H.Kim, E.Kim, K.J.Lee, Y.H.Jeon, and E.E.Kim (2009).
Structure and interaction of ubiquitin-associated domain of human Fas-associated factor 1.
  Protein Sci, 18, 2265-2276.  
19034675 R.Schmucki, S.Yokoyama, and P.Güntert (2009).
Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm.
  J Biomol NMR, 43, 97.  
19450525 V.Kirkin, D.G.McEwan, I.Novak, and I.Dikic (2009).
A role for ubiquitin in selective autophagy.
  Mol Cell, 34, 259-269.  
19749745 Y.Yoshikawa, M.Ogawa, T.Hain, M.Yoshida, M.Fukumatsu, M.Kim, H.Mimuro, I.Nakagawa, T.Yanagawa, T.Ishii, A.Kakizuka, E.Sztul, T.Chakraborty, and C.Sasakawa (2009).
Listeria monocytogenes ActA-mediated escape from autophagic recognition.
  Nat Cell Biol, 11, 1233-1240.  
19032921 M.Seton (2008).
Paget's disease: epidemiology and pathophysiology.
  Curr Osteoporos Rep, 6, 125-129.  
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.