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PDBsum entry 1aar
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protein Protein-protein interface(s) links
Ubiquitin PDB id
1aar

 

 

 

 

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Contents
Protein chains
76 a.a. *
Waters ×15
* Residue conservation analysis
PDB id:
1aar
Name: Ubiquitin
Title: Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (e2)
Structure: Di-ubiquitin. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.190    
Authors: W.J.Cook,L.C.Jeffrey,M.Carson,Z.Chen,C.M.Pickart
Key ref: W.J.Cook et al. (1992). Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2). J Biol Chem, 267, 16467-16471. PubMed id: 1322903
Date:
17-Apr-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0CH28  (UBC_BOVIN) -  Polyubiquitin-C from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		690 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
J Biol Chem 267:16467-16471 (1992)
PubMed id: 1322903  
 
 
Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2).
W.J.Cook, L.C.Jeffrey, M.Carson, Z.Chen, C.M.Pickart.
 
  ABSTRACT  
 
Covalent ligation of multiubiquitin chains targets eukaryotic proteins for degradation. In such multiubiquitin chains, successive ubiquitins are linked by an isopeptide bond involving the side chain of Lys48 and the carboxyl group of Gly76. The crystal structure of a diubiquitin conjugate has been determined and refined at 2.3-A resolution. The molecule has internal approximate 2-fold symmetry with multiple hydrophobic and hydrophilic contacts along the 2-fold axis. The structure of the diubiquitin conjugate suggests determinants for recognition of multiubiquitin chains. A model for the interaction of diubiquitin and a ubiquitin conjugating enzyme (E2) is proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22237024 G.C.Lander, E.Estrin, M.E.Matyskiela, C.Bashore, E.Nogales, and A.Martin (2012).
Complete subunit architecture of the proteasome regulatory particle.
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22334143 L.Davis, and J.W.Chin (2012).
Designer proteins: applications of genetic code expansion in cell biology.
  Nat Rev Mol Cell Biol, 13, 168-182.  
22820888 Y.Kulathu, and D.Komander (2012).
Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages.
  Nat Rev Mol Cell Biol, 13, 508-523.  
23201676 Y.Ye, G.Blaser, M.H.Horrocks, M.J.Ruedas-Rama, S.Ibrahim, A.A.Zhukov, A.Orte, D.Klenerman, S.E.Jackson, and D.Komander (2012).
Ubiquitin chain conformation regulates recognition and activity of interacting proteins.
  Nature, 492, 266-270.  
21212884 C.A.Castañeda, J.Liu, T.R.Kashyap, R.K.Singh, D.Fushman, and T.A.Cropp (2011).
Controlled enzymatic synthesis of natural-linkage, defined-length polyubiquitin chains using lysines with removable protecting groups.
  Chem Commun (Camb), 47, 2026-2028.  
20524020 P.Mitra, and D.Pal (2011).
dockYard-a repository to assist modeling of protein-protein docking.
  J Mol Model, 17, 599-606.  
19853612 D.Fushman, and O.Walker (2010).
Exploring the linkage dependence of polyubiquitin conformations using molecular modeling.
  J Mol Biol, 395, 803-814.  
  20823512 J.F.Trempe, N.R.Brown, M.E.Noble, and J.A.Endicott (2010).
A new crystal form of Lys48-linked diubiquitin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 994-998.
PDB code: 3m3j
20802491 S.Virdee, Y.Ye, D.P.Nguyen, D.Komander, and J.W.Chin (2010).
Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase.
  Nat Chem Biol, 6, 750-757.
PDB code: 2xk5
19243136 F.E.Reyes-Turcu, and K.D.Wilkinson (2009).
Polyubiquitin binding and disassembly by deubiquitinating enzymes.
  Chem Rev, 109, 1495-1508.  
19811316 F.Zhou (2009).
Molecular mechanisms of viral immune evasion proteins to inhibit MHC class I antigen processing and presentation.
  Int Rev Immunol, 28, 376-393.  
20003470 I.A.Qureshi, F.Ferron, C.C.Seh, P.Cheung, and J.Lescar (2009).
Crystallographic structure of ubiquitin in complex with cadmium ions.
  BMC Res Notes, 2, 251.
PDB code: 3h1u
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.  
19541633 S.Garcia-Manyes, L.Dougan, and J.M.Fernández (2009).
Osmolyte-induced separation of the mechanical folding phases of ubiquitin.
  Proc Natl Acad Sci U S A, 106, 10540-10545.  
18599482 B.J.Winborn, S.M.Travis, S.V.Todi, K.M.Scaglione, P.Xu, A.J.Williams, R.E.Cohen, J.Peng, and H.L.Paulson (2008).
The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits Lys63 linkages in mixed linkage ubiquitin chains.
  J Biol Chem, 283, 26436-26443.  
18724939 K.Newton, M.L.Matsumoto, I.E.Wertz, D.S.Kirkpatrick, J.R.Lill, J.Tan, D.Dugger, N.Gordon, S.S.Sidhu, F.A.Fellouse, L.Komuves, D.M.French, R.E.Ferrando, C.Lam, D.Compaan, C.Yu, I.Bosanac, S.G.Hymowitz, R.F.Kelley, and V.M.Dixit (2008).
Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.
  Cell, 134, 668-678.
PDB codes: 3dvg 3dvn
18588675 L.Sanchez-Pulido, D.Devos, Z.R.Sung, and M.Calonje (2008).
RAWUL: a new ubiquitin-like domain in PRC1 ring finger proteins that unveils putative plant and worm PRC1 orthologs.
  BMC Genomics, 9, 308.  
18790135 Q.Zhang, E.Crosland, and D.Fabris (2008).
Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies.
  Anal Chim Acta, 627, 117-128.  
18438605 W.Li, and Y.Ye (2008).
Polyubiquitin chains: functions, structures, and mechanisms.
  Cell Mol Life Sci, 65, 2397-2406.  
17496917 A.Adhikari, M.Xu, and Z.J.Chen (2007).
Ubiquitin-mediated activation of TAK1 and IKK.
  Oncogene, 26, 3214-3226.  
17242378 B.C.Dickinson, R.Varadan, and D.Fushman (2007).
Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin.
  Protein Sci, 16, 369-378.  
  18062814 K.K.Durston, D.K.Chiu, D.L.Abel, and J.T.Trevors (2007).
Measuring the functional sequence complexity of proteins.
  Theor Biol Med Model, 4, 47.  
17355622 T.Woelk, S.Sigismund, L.Penengo, and S.Polo (2007).
The ubiquitination code: a signalling problem.
  Cell Div, 2, 11.  
17319663 Y.E.Ryabov, and D.Fushman (2007).
A model of interdomain mobility in a multidomain protein.
  J Am Chem Soc, 129, 3315-3327.  
17550252 Y.Ryabov, and D.Fushman (2007).
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
  J Am Chem Soc, 129, 7894-7902.
PDB codes: 2pe9 2pea
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
16823894 Y.Ryabov, and D.Fushman (2006).
Analysis of interdomain dynamics in a two-domain protein using residual dipolar couplings together with 15N relaxation data.
  Magn Reson Chem, 44, S143-S151.  
16609980 Y.Ryabov, and D.Fushman (2006).
Interdomain mobility in di-ubiquitin revealed by NMR.
  Proteins, 63, 787-796.  
15937902 A.D.van Dijk, D.Fushman, and A.M.Bonvin (2005).
Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
  Proteins, 60, 367-381.
PDB code: 2bgf
15837191 A.Ohno, J.Jee, K.Fujiwara, T.Tenno, N.Goda, H.Tochio, H.Kobayashi, H.Hiroaki, and M.Shirakawa (2005).
Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition.
  Structure, 13, 521-532.
PDB code: 1wr1
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
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
15556404 C.M.Pickart, and D.Fushman (2004).
Polyubiquitin chains: polymeric protein signals.
  Curr Opin Chem Biol, 8, 610-616.  
15461659 T.Tenno, K.Fujiwara, H.Tochio, K.Iwai, E.H.Morita, H.Hayashi, S.Murata, H.Hiroaki, M.Sato, K.Tanaka, and M.Shirakawa (2004).
Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains.
  Genes Cells, 9, 865-875.  
15029246 X.Yuan, P.Simpson, C.McKeown, H.Kondo, K.Uchiyama, R.Wallis, I.Dreveny, C.Keetch, X.Zhang, C.Robinson, P.Freemont, and S.Matthews (2004).
Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97.
  EMBO J, 23, 1463-1473.
PDB codes: 1v92 1vaz
12052895 L.Chen, and K.Madura (2002).
Rad23 promotes the targeting of proteolytic substrates to the proteasome.
  Mol Cell Biol, 22, 4902-4913.  
12056889 M.Sundd, N.Iverson, B.Ibarra-Molero, J.M.Sanchez-Ruiz, and A.D.Robertson (2002).
Electrostatic interactions in ubiquitin: stabilization of carboxylates by lysine amino groups.
  Biochemistry, 41, 7586-7596.  
11173499 C.L.Phillips, J.Thrower, C.M.Pickart, and C.P.Hill (2001).
Structure of a new crystal form of tetraubiquitin.
  Acta Crystallogr D Biol Crystallogr, 57, 341-344.
PDB code: 1f9j
10872471 D.Voges, P.Zwickl, and W.Baumeister (1999).
The 26S proteasome: a molecular machine designed for controlled proteolysis.
  Annu Rev Biochem, 68, 1015-1068.  
  8740525 C.J.Tsai, S.L.Lin, H.J.Wolfson, and R.Nussinov (1996).
Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences.
  Crit Rev Biochem Mol Biol, 31, 127-152.  
8570649 R.Beal, Q.Deveraux, G.Xia, M.Rechsteiner, and C.Pickart (1996).
Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting.
  Proc Natl Acad Sci U S A, 93, 861-866.  
7788293 A.E.Sauer-Eriksson, G.J.Kleywegt, M.Uhlén, and T.A.Jones (1995).
Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG.
  Structure, 3, 265-278.
PDB code: 1fcc
  7862120 J.Spence, S.Sadis, A.L.Haas, and D.Finley (1995).
A ubiquitin mutant with specific defects in DNA repair and multiubiquitination.
  Mol Cell Biol, 15, 1265-1273.  
  7663344 M.D.Cummings, T.N.Hart, and R.J.Read (1995).
Monte Carlo docking with ubiquitin.
  Protein Sci, 4, 885-899.  
  8535245 M.D.Cummings, T.N.Hart, and R.J.Read (1995).
Atomic solvation parameters in the analysis of protein-protein docking results.
  Protein Sci, 4, 2087-2099.  
  8035826 D.Finley, S.Sadis, B.P.Monia, P.Boucher, D.J.Ecker, S.T.Crooke, and V.Chau (1994).
Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant.
  Mol Cell Biol, 14, 5501-5509.  
  7969127 T.Arnason, and M.J.Ellison (1994).
Stress resistance in Saccharomyces cerevisiae is strongly correlated with assembly of a novel type of multiubiquitin chain.
  Mol Cell Biol, 14, 7876-7883.  
8393731 P.Chen, P.Johnson, T.Sommer, S.Jentsch, and M.Hochstrasser (1993).
Multiple ubiquitin-conjugating enzymes participate in the in vivo degradation of the yeast MAT alpha 2 repressor.
  Cell, 74, 357-369.  
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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