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PDBsum entry 1wr1
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protein Protein-protein interface(s) links
Signaling protein PDB id
1wr1

 

 

 

 

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Contents
Protein chains
76 a.a. *
58 a.a. *
* Residue conservation analysis
PDB id:
1wr1
Name: Signaling protein
Title: The complex structure of dsk2p uba with ubiquitin
Structure: Ubiquitin. Chain: a. Engineered: yes. Ubiquitin-like protein dsk2. Chain: b. Fragment: c-terminal uba domain. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ubi4 (1224-1451). Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: dsk2 (982-1120).
NMR struc: 20 models
Authors: A.Ohno,J.G.Jee,K.Fujiwara,T.Tenno,N.Goda,H.Tochio,H.Hiroaki, H.Kobayashi,M.Shirakawa
Key ref:
A.Ohno et al. (2005). Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Structure, 13, 521-532. PubMed id: 15837191 DOI: 10.1016/j.str.2005.01.011
Date:
08-Oct-04     Release date:   19-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0CG63  (UBI4P_YEAST) -  Polyubiquitin from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		381 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P48510  (DSK2_YEAST) -  Ubiquitin domain-containing protein DSK2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		373 a.a.
58 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 

 
DOI no: 10.1016/j.str.2005.01.011 Structure 13:521-532 (2005)
PubMed id: 15837191  
 
 
Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition.
A.Ohno, J.Jee, K.Fujiwara, T.Tenno, N.Goda, H.Tochio, H.Kobayashi, H.Hiroaki, M.Shirakawa.
 
  ABSTRACT  
 
The ubiquitin-associated (UBA) domain is one of the most frequently occurring motifs that recognize ubiquitin tags. Dsk2p, a UBA-containing protein from Saccharomyces cerevisiae, is involved in the ubiquitin-proteasome proteolytic pathway and has been implicated in spindle pole duplication. Here we present the solution structure of the UBA domain of Dsk2p (Dsk2(UBA)) in complex with ubiquitin. The structure reveals that the UBA domain uses a mode of ubiquitin recognition that is similar to that of the CUE domain, another ubiquitin binding motif that shares low sequence homology but high structural similarity with UBA domains. These two domains, as well as the structurally unrelated ubiquitin binding motif UIM, provide a common, crucial recognition site for ubiquitin, comprising a hydrogen-bonding acceptor for the amide group of Gly-47, and a methyl group that packs against the hydrophobic pocket of ubiquitin formed by Leu-8, Ile-44, His-68, and Val-70.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Comparison of UBA Domains
Ribbon diagrams comparing the ubiquitin bound Dsk2^UBA (red) and two unliganded UBA domains: the N-terminal UBA domain of hHR23A^UBA1 (PDB code 1IFY; orange) and the UBA domain of rat p47^UBA (PDB code 1V92; pink). The side chains of conserved residues, which are important for formation of the hydrophobic core and structural integrity, are indicated in yellow. These residues correspond to those shown in yellow font in Figure 1.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 521-532) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20026602 A.A.Ogunjimi, S.Wiesner, D.J.Briant, X.Varelas, F.Sicheri, J.Forman-Kay, and J.L.Wrana (2010).
The ubiquitin binding region of the Smurf HECT domain facilitates polyubiquitylation and binding of ubiquitylated substrates.
  J Biol Chem, 285, 6308-6315.  
20949063 A.X.Song, C.J.Zhou, Y.Peng, X.C.Gao, Z.R.Zhou, Q.S.Fu, J.Hong, D.H.Lin, and H.Y.Hu (2010).
Structural transformation of the tandem ubiquitin-interacting motifs in ataxin-3 and their cooperative interactions with ubiquitin chains.
  PLoS One, 5, e13202.  
20854370 C.A.Lamb, R.K.McCann, J.Stöckli, D.E.James, and N.J.Bryant (2010).
Insulin-regulated trafficking of GLUT4 requires ubiquitination.
  Traffic, 11, 1445-1454.  
20739285 C.Riedinger, J.Boehringer, J.F.Trempe, E.D.Lowe, N.R.Brown, K.Gehring, M.E.Noble, C.Gordon, and J.A.Endicott (2010).
Structure of Rpn10 and its interactions with polyubiquitin chains and the proteasome subunit Rpn12.
  J Biol Chem, 285, 33992-34003.
PDB code: 2x5n
20127391 F.Kieken, G.Spagnol, V.Su, A.F.Lau, and P.L.Sorgen (2010).
NMR structure note: UBA domain of CIP75.
  J Biomol NMR, 46, 245-250.
PDB code: 2knz
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.  
20399133 H.Fu, Y.L.Lin, and A.S.Fatimababy (2010).
Proteasomal recognition of ubiquitylated substrates.
  Trends Plant Sci, 15, 375-386.  
20159559 M.G.Bomar, S.D'Souza, M.Bienko, I.Dikic, G.C.Walker, and P.Zhou (2010).
Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1.
  Mol Cell, 37, 408-417.
PDB code: 2khu
20064467 D.Zhang, T.Chen, I.Ziv, R.Rosenzweig, Y.Matiuhin, V.Bronner, M.H.Glickman, and D.Fushman (2009).
Together, Rpn10 and Dsk2 can serve as a polyubiquitin chain-length sensor.
  Mol Cell, 36, 1018-1033.  
19382171 G.Nicastro, L.Masino, V.Esposito, R.P.Menon, A.De Simone, F.Fraternali, and A.Pastore (2009).
Josephin domain of ataxin-3 contains two distinct ubiquitin-binding sites.
  Biopolymers, 91, 1203-1214.  
19773779 I.Dikic, S.Wakatsuki, and K.J.Walters (2009).
Ubiquitin-binding domains - from structures to functions.
  Nat Rev Mol Cell Biol, 10, 659-671.  
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.  
19401465 M.Hobeika, C.Brockmann, F.Gruessing, D.Neuhaus, G.Divita, M.Stewart, and C.Dargemont (2009).
Structural requirements for the ubiquitin-associated domain of the mRNA export factor Mex67 to bind its specific targets, the transcription elongation THO complex component Hpr1 and nucleoporin FXFG repeats.
  J Biol Chem, 284, 17575-17583.
PDB code: 2khh
18241885 D.Zhang, S.Raasi, and D.Fushman (2008).
Affinity makes the difference: nonselective interaction of the UBA domain of Ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains.
  J Mol Biol, 377, 162-180.
PDB codes: 2jy5 2jy6
18482987 F.E.Reyes-Turcu, J.R.Shanks, D.Komander, and K.D.Wilkinson (2008).
Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T.
  J Biol Chem, 283, 19581-19592.  
18160718 L.Chen, and K.Madura (2008).
Centrin/Cdc31 is a novel regulator of protein degradation.
  Mol Cell Biol, 28, 1829-1840.  
18931663 M.Gyrd-Hansen, M.Darding, M.Miasari, M.M.Santoro, L.Zender, W.Xue, T.Tenev, P.C.da Fonseca, M.Zvelebil, J.M.Bujnicki, S.Lowe, J.Silke, and P.Meier (2008).
IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.
  Nat Cell Biol, 10, 1309-1317.  
18497827 P.Schreiner, X.Chen, K.Husnjak, L.Randles, N.Zhang, S.Elsasser, D.Finley, I.Dikic, K.J.Walters, and M.Groll (2008).
Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction.
  Nature, 453, 548-552.
PDB codes: 2r2y 2z59
19636891 T.Chen, D.Zhang, Y.Matiuhin, M.Glickman, and D.Fushman (2008).
1H, 13C, and 15N resonance assignment of the ubiquitin-like domain from Dsk2p.
  Biomol NMR Assign, 2, 147-149.  
18083189 Y.C.Kim, and G.Hummer (2008).
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
  J Mol Biol, 375, 1416-1433.  
17679096 A.Mikhailik, B.Ford, J.Keller, Y.Chen, N.Nassar, and N.Carpino (2007).
A phosphatase activity of Sts-1 contributes to the suppression of TCR signaling.
  Mol Cell, 27, 486-497.
PDB codes: 2h0q 2ikq
17897937 G.Kozlov, L.Nguyen, T.Lin, G.De Crescenzo, M.Park, and K.Gehring (2007).
Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD.
  J Biol Chem, 282, 35787-35795.
PDB code: 2qho
17475778 M.Hobeika, C.Brockmann, N.Iglesias, C.Gwizdek, D.Neuhaus, F.Stutz, M.Stewart, G.Divita, and C.Dargemont (2007).
Coordination of Hpr1 and ubiquitin binding by the UBA domain of the mRNA export factor Mex67.
  Mol Biol Cell, 18, 2561-2568.
PDB code: 2jp7
17567738 N.B.de la Cruz, F.C.Peterson, B.L.Lytle, and B.F.Volkman (2007).
Solution structure of a membrane-anchored ubiquitin-fold (MUB) protein from Homo sapiens.
  Protein Sci, 16, 1479-1484.
PDB code: 2gow
17679095 P.Peschard, G.Kozlov, T.Lin, I.A.Mirza, A.M.Berghuis, S.Lipkowitz, M.Park, and K.Gehring (2007).
Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b.
  Mol Cell, 27, 474-485.
PDB codes: 2ooa 2oob
16803889 A.Marx, C.Nugoor, J.Müller, S.Panneerselvam, T.Timm, M.Bilang, E.Mylonas, D.I.Svergun, E.M.Mandelkow, and E.Mandelkow (2006).
Structural variations in the catalytic and ubiquitin-associated domains of microtubule-associated protein/microtubule affinity regulating kinase (MARK) 1 and MARK2.
  J Biol Chem, 281, 27586-27599.
PDB code: 2hak
16421449 E.D.Lowe, N.Hasan, J.F.Trempe, L.Fonso, M.E.Noble, J.A.Endicott, L.N.Johnson, and N.R.Brown (2006).
Structures of the Dsk2 UBL and UBA domains and their complex.
  Acta Crystallogr D Biol Crystallogr, 62, 177-188.
PDB codes: 2bwb 2bwe 2bwf
16564012 F.E.Reyes-Turcu, J.R.Horton, J.E.Mullally, A.Heroux, X.Cheng, and K.D.Wilkinson (2006).
The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin.
  Cell, 124, 1197-1208.
PDB codes: 2g43 2g45
16499958 L.Penengo, M.Mapelli, A.G.Murachelli, S.Confalonieri, L.Magri, A.Musacchio, P.P.Di Fiore, S.Polo, and T.R.Schneider (2006).
Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin.
  Cell, 124, 1183-1195.
PDB codes: 2c7m 2c7n
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
16462748 S.Hirano, M.Kawasaki, H.Ura, R.Kato, C.Raiborg, H.Stenmark, and S.Wakatsuki (2006).
Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting.
  Nat Struct Mol Biol, 13, 272-277.
PDB code: 2d3g
17031531 T.Sakai, H.Tochio, T.Tenno, Y.Ito, T.Kokubo, H.Hiroaki, and M.Shirakawa (2006).
In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes.
  J Biomol NMR, 36, 179-188.  
16731964 Y.G.Chang, A.X.Song, Y.G.Gao, Y.H.Shi, X.J.Lin, X.T.Cao, D.H.Lin, and H.Y.Hu (2006).
Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin.
  Protein Sci, 15, 1248-1259.
PDB codes: 2cwb 2den
16138082 J.F.Trempe, N.R.Brown, E.D.Lowe, C.Gordon, I.D.Campbell, M.E.Noble, and J.A.Endicott (2005).
Mechanism of Lys48-linked polyubiquitin chain recognition by the Mud1 UBA domain.
  EMBO J, 24, 3178-3189.
PDB code: 1z96
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
15949443 R.Varadan, M.Assfalg, S.Raasi, C.Pickart, and D.Fushman (2005).
Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain.
  Mol Cell, 18, 687-698.
PDB code: 1zo6
16007098 S.Raasi, R.Varadan, D.Fushman, and C.M.Pickart (2005).
Diverse polyubiquitin interaction properties of ubiquitin-associated domains.
  Nat Struct Mol Biol, 12, 708-714.  
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 code is shown on the right.

 

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