PDBsum entry 1cmx

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protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
214 a.a. *
76 a.a. *
17 a.a. *
Waters ×75
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structural basis for the specificity of ubiquitin c- terminal hydrolases
Structure: Protein (ubiquitin yuh1-ubal). Chain: a, c. Fragment: all. Engineered: yes. Other_details: ubiquitin c-terminus modified to an aldehyde. Protein (ubiquitin yuh1-ubal). Chain: b, d. Fragment: all.
Source: Synthetic: yes. Other_details: the protein was chemically synthesized. The sequence of this protein is naturally found in the cytoplasm of plasmid p-1a2/trpyuh1-1 of saccharomyces cerevisiae (baker's yeast). The expression system was escherichia coli, strain mm294, plasmid p-1a2/trpyuh1-1.. Escherichia coli, strain mm294, plasmid p-1a2/trpyuh1-1.
Biol. unit: Tetramer (from PQS)
2.25Å     R-factor:   0.248     R-free:   0.285
Authors: S.C.Johnston,S.M.Riddle,R.E.Cohen,C.P.Hill
Key ref:
S.C.Johnston et al. (1999). Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J, 18, 3877-3887. PubMed id: 10406793 DOI: 10.1093/emboj/18.14.3877
12-May-99     Release date:   27-Jul-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P35127  (UBL1_YEAST) -  Ubiquitin carboxyl-terminal hydrolase YUH1
236 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C
685 a.a.
76 a.a.*
Protein chain
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C
685 a.a.
17 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, C: E.C.  - Ubiquitinyl hydrolase 1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     ubiquitin homeostasis   2 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1093/emboj/18.14.3877 EMBO J 18:3877-3887 (1999)
PubMed id: 10406793  
Structural basis for the specificity of ubiquitin C-terminal hydrolases.
S.C.Johnston, S.M.Riddle, R.E.Cohen, C.P.Hill.
The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.
  Selected figure(s)  
Figure 1.
Figure 1 Stereoview ribbon representation of the Yuh1–Ubal complex. (A) Ubal is not shown in this panel. Sidechains of the active-site residues Gln84, Cys90, His166 and Asp181 (red) are labeled Q, C, H and D. N- and C-termini are labeled. The disordered segment (residues 63–77) is indicated with the adjacent ordered residues labeled in magenta. The active-site-crossover loop is colored yellow. Secondary structures were as defined by PROMOTIF (Hutchinson and Thornton, 1996). Strands are colored green and the helices blue. Helix 4, which contains the active-site nucleophile Cys90, is colored cyan. This helix undergoes a severe kink, indeed PROMOTIF defines residues 90–100 and 103–105 as separate helices. We describe this as one continuous helix in order to maintain consistency of nomenclature with UCH-L3, which also has a severe kink in the corresponding part of helix 4. The following are labeled on the figure: strand 0 (S0, residues 11–12), strand 1 (S1, 31–36), strand 2 (S2, 54–60), strand 2^1 (S2^1, 81–82), strand 2^2 (S2^2, 128–129), strand 3 (S3, 165–172), strand 4 (S4, 176–180), strand 5 (S5, 189–193), strand 6 (S6, 227–233); helix 1 (H1, residues 15–25), helix 2 (H2, 44–46), helix 4 (H4, 90–105), helix 5 (H5, 111–122), helix 6 (H6, 132–143), helix 7 (H7, 205–221). Helices are alpha-type, except for helix 2 and residues 102–105 of helix 4, which adopt the 3[10] conformation. There is a turn of alpha helix (residues 146–150) within the active-site-crossover loop. (B) Same as (A), but including the Ubal shown in magenta. The sidechains of Ubal residues discussed in the text are shown in orange and labeled. Figures 1, 4, 5 and 6 were produced with the programs MOLSCRIPT (Kraulis, 1991) and RASTER 3D (Bacon and Anderson, 1988).
Figure 3.
Figure 3 Schematic of the UCH/cysteine protease reaction cycle. TI-1 and TI-2 denote the high energy tetrahedral intermediates; AI, the acyl intermediate; S, a cysteine; and Im, a histidine. Adapted from Storer and Ménard (1994).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 3877-3887) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21135870 C.Zheng, Q.Yin, and H.Wu (2011).
Structural studies of NF-κB signaling.
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Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.
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PDB codes: 3ifw 3irt 3kvf 3kw5
19266312 H.Y.Yeh, and P.H.Klesius (2010).
Characterization and tissue expression of channel catfish (Ictalurus punctatus Rafinesque, 1818) ubiquitin carboxyl-terminal hydrolase L5 (UCHL5) cDNA.
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Characterization and structural studies of the Plasmodium falciparum ubiquitin and Nedd8 hydrolase UCHL3.
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PDB codes: 2wdt 2we6
20384815 M.C.Liu, L.Akinyi, D.Scharf, J.Mo, S.F.Larner, U.Muller, M.W.Oli, W.Zheng, F.Kobeissy, L.Papa, X.C.Lu, J.R.Dave, F.C.Tortella, R.L.Hayes, and K.K.Wang (2010).
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Crystal structure of the peptidase domain of Streptococcus ComA, a bifunctional ATP-binding cassette transporter involved in the quorum-sensing pathway.
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PDB code: 3k8u
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PDB codes: 2jf5 2w9n
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19243136 F.E.Reyes-Turcu, and K.D.Wilkinson (2009).
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Untangling the folding mechanism of the 5-knotted protein UCH-L3.
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A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves.
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Josephin domain of ataxin-3 contains two distinct ubiquitin-binding sites.
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19864628 M.W.Foster, M.T.Forrester, and J.S.Stamler (2009).
A protein microarray-based analysis of S-nitrosylation.
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19047059 M.W.Popp, K.Artavanis-Tsakonas, and H.L.Ploegh (2009).
Substrate Filtering by the Active Site Crossover Loop in UCHL3 Revealed by Sortagging and Gain-of-function Mutations.
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19251672 T.S.Kroeger, K.P.Watkins, G.Friso, K.J.van Wijk, and A.Barkan (2009).
A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing.
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18276160 A.M.Burroughs, M.Jaffee, L.M.Iyer, and L.Aravind (2008).
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18802447 G.Rabut, and M.Peter (2008).
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18652489 J.Souphron, M.B.Waddell, A.Paydar, Z.Tokgöz-Gromley, M.F.Roussel, and B.A.Schulman (2008).
Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1.
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PDB codes: 3dbh 3dbl 3dbr
18687060 K.H.Ventii, and K.D.Wilkinson (2008).
Protein partners of deubiquitinating enzymes.
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18346885 L.Song, and M.Rape (2008).
Reverse the curse--the role of deubiquitination in cell cycle control.
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18523727 N.A.Lakomek, K.F.Walter, C.Farès, O.F.Lange, Groot, H.Grubmüller, R.Brüschweiler, A.Munk, S.Becker, J.Meiler, and C.Griesinger (2008).
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PDB code: 3dkb
18550537 T.Kabuta, A.Furuta, S.Aoki, K.Furuta, and K.Wada (2008).
Aberrant Interaction between Parkinson Disease-associated Mutant UCH-L1 and the Lysosomal Receptor for Chaperone-mediated Autophagy.
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18922472 T.Yao, L.Song, J.Jin, Y.Cai, H.Takahashi, S.K.Swanson, M.P.Washburn, L.Florens, R.C.Conaway, R.E.Cohen, and J.W.Conaway (2008).
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18485060 Y.Liu, F.Wang, H.Zhang, H.He, L.Ma, and X.W.Deng (2008).
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17919899 A.D.Capili, and C.D.Lima (2007).
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17651432 A.Fernández-Montalván, T.Bouwmeester, G.Joberty, R.Mader, M.Mahnke, B.Pierrat, J.M.Schlaeppi, S.Worpenberg, and B.Gerhartz (2007).
Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization.
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17446860 C.Richter, M.West, and G.Odorizzi (2007).
Dual mechanisms specify Doa4-mediated deubiquitination at multivesicular bodies.
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17349955 C.Schlieker, W.A.Weihofen, E.Frijns, L.M.Kattenhorn, R.Gaudet, and H.L.Ploegh (2007).
Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes.
  Mol Cell, 25, 677-687.
PDB code: 2j7q
17371404 E.M.Frickel, V.Quesada, L.Muething, M.J.Gubbels, E.Spooner, H.Ploegh, and K.Artavanis-Tsakonas (2007).
Apicomplexan UCHL3 retains dual specificity for ubiquitin and Nedd8 throughout evolution.
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17259170 R.K.Meray, and P.T.Lansbury (2007).
Reversible monoubiquitination regulates the Parkinson disease-associated ubiquitin hydrolase UCH-L1.
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Putting proteomics on target: activity-based profiling of ubiquitin and ubiquitin-like processing enzymes.
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Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1.
  Proc Natl Acad Sci U S A, 103, 4675-4680.
PDB code: 2etl
17099700 D.Reverter, and C.D.Lima (2006).
Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.
  Nat Struct Mol Biol, 13, 1060-1068.
PDB codes: 2io0 2io1 2io2 2io3
17146457 D.T.Huang, and B.A.Schulman (2006).
Breaking up with a kinky SUMO.
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17096206 G.Nicastro, M.Habeck, L.Masino, D.I.Svergun, and A.Pastore (2006).
Structure validation of the Josephin domain of ataxin-3: conclusive evidence for an open conformation.
  J Biomol NMR, 36, 267-277.  
16356462 J.J.Arnold, A.Bernal, U.Uche, D.E.Sterner, T.R.Butt, C.E.Cameron, and M.R.Mattern (2006).
Small ubiquitin-like modifying protein isopeptidase assay based on poliovirus RNA polymerase activity.
  Anal Biochem, 350, 214-221.  
17099698 L.Shen, M.H.Tatham, C.Dong, A.Zagórska, J.H.Naismith, and R.T.Hay (2006).
SUMO protease SENP1 induces isomerization of the scissile peptide bond.
  Nat Struct Mol Biol, 13, 1069-1077.
PDB codes: 2iy0 2iy1
16978047 P.Virnau, L.A.Mirny, and M.Kardar (2006).
Intricate knots in proteins: Function and evolution.
  PLoS Comput Biol, 2, e122.  
16377622 S.Ishii, T.Yano, and H.Hayashi (2006).
Expression and characterization of the peptidase domain of Streptococcus pneumoniae ComA, a bifunctional ATP-binding cassette transporter involved in quorum sensing pathway.
  J Biol Chem, 281, 4726-4731.  
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.  
16913834 T.Sulea, H.A.Lindner, and R.Ménard (2006).
Structural aspects of recently discovered viral deubiquitinating activities.
  Biol Chem, 387, 853-862.  
16906146 T.Yao, L.Song, W.Xu, G.N.DeMartino, L.Florens, S.K.Swanson, M.P.Washburn, R.C.Conaway, J.W.Conaway, and R.E.Cohen (2006).
Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1.
  Nat Cell Biol, 8, 994.  
16020535 G.Nicastro, R.P.Menon, L.Masino, P.P.Knowles, N.Q.McDonald, and A.Pastore (2005).
The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition.
  Proc Natl Acad Sci U S A, 102, 10493-10498.
PDB code: 1yzb
16306591 H.A.Lindner, N.Fotouhi-Ardakani, V.Lytvyn, P.Lachance, T.Sulea, and R.Ménard (2005).
The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme.
  J Virol, 79, 15199-15208.  
16091470 I.A.Rose (2005).
Ubiquitin at Fox Chase.
  Proc Natl Acad Sci U S A, 102, 11575-11577.  
16094396 I.Rose (2005).
Ubiquitin at Fox Chase.
  Cell Death Differ, 12, 1198-1201.  
16142821 I.Rose (2005).
Ubiquitin at Fox Chase (Nobel lecture).
  Angew Chem Int Ed Engl, 44, 5926-5931.  
16183633 K.Sugawara, N.N.Suzuki, Y.Fujioka, N.Mizushima, Y.Ohsumi, and F.Inagaki (2005).
Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy.
  J Biol Chem, 280, 40058-40065.
PDB code: 2cy7
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
15775960 L.N.Shen, H.Liu, C.Dong, D.Xirodimas, J.H.Naismith, and R.T.Hay (2005).
Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1.
  EMBO J, 24, 1341-1351.
PDB codes: 2bkq 2bkr
16211010 M.Hu, P.Li, L.Song, P.D.Jeffrey, T.A.Chenova, K.D.Wilkinson, R.E.Cohen, and Y.Shi (2005).
Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14.
  EMBO J, 24, 3747-3756.
PDB codes: 2ayn 2ayo
16306590 N.Barretto, D.Jukneliene, K.Ratia, Z.Chen, A.D.Mesecar, and S.C.Baker (2005).
The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity.
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15531586 S.Misaghi, P.J.Galardy, W.J.Meester, H.Ovaa, H.L.Ploegh, and R.Gaudet (2005).
Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate.
  J Biol Chem, 280, 1512-1520.
PDB code: 1xd3
16118278 Y.Mao, F.Senic-Matuglia, P.P.Di Fiore, S.Polo, M.E.Hodsdon, and P.De Camilli (2005).
Deubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain.
  Proc Natl Acad Sci U S A, 102, 12700-12705.
PDB code: 2aga
14581483 A.Guterman, and M.H.Glickman (2004).
Complementary roles for Rpn11 and Ubp6 in deubiquitination and proteolysis by the proteasome.
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15096636 A.M.Catanzariti, T.A.Soboleva, D.A.Jans, P.G.Board, and R.T.Baker (2004).
An efficient system for high-level expression and easy purification of authentic recombinant proteins.
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15296745 D.Reverter, and C.D.Lima (2004).
A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex.
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PDB codes: 1tgz 1th0
15361859 D.T.Huang, D.W.Miller, R.Mathew, R.Cassell, J.M.Holton, M.F.Roussel, and B.A.Schulman (2004).
A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8.
  Nat Struct Mol Biol, 11, 927-935.
PDB code: 1tt5
14673145 J.Hemelaar, A.Borodovsky, B.M.Kessler, D.Reverter, J.Cook, N.Kolli, T.Gan-Erdene, K.D.Wilkinson, G.Gill, C.D.Lima, H.L.Ploegh, and H.Ovaa (2004).
Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins.
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15265035 M.Albrecht, M.Golatta, U.Wüllner, and T.Lengauer (2004).
Structural and functional analysis of ataxin-2 and ataxin-3.
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Crystal structure of human otubain 2.
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PDB code: 1tff
14737182 X.I.Ambroggio, D.C.Rees, and R.J.Deshaies (2004).
JAMM: a metalloprotease-like zinc site in the proteasome and signalosome.
  PLoS Biol, 2, E2.
PDB code: 1r5x
12660720 A.P.VanDemark, and C.P.Hill (2003).
Two-stepping with E1.
  Nat Struct Biol, 10, 244-246.  
12944097 B.R.Wong, F.Parlati, K.Qu, S.Demo, T.Pray, J.Huang, D.G.Payan, and M.K.Bennett (2003).
Drug discovery in the ubiquitin regulatory pathway.
  Drug Discov Today, 8, 746-754.  
12517332 C.D.Lima (2003).
Regulating UBP-mediated ubiquitin deconjugation.
  Structure, 11, 3-4.  
14530254 J.Hemelaar, V.S.Lelyveld, B.M.Kessler, and H.L.Ploegh (2003).
A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L.
  J Biol Chem, 278, 51841-51850.  
12833545 M.Sulpizi, A.Laio, J.VandeVondele, A.Cattaneo, U.Rothlisberger, and P.Carloni (2003).
Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.
  Proteins, 52, 212-224.  
12668429 M.Sulpizi, U.Rothlisberger, and P.Carloni (2003).
Molecular dynamics studies of caspase-3.
  Biophys J, 84, 2207-2215.  
12704427 M.Y.Balakirev, S.O.Tcherniuk, M.Jaquinod, and J.Chroboczek (2003).
Otubains: a new family of cysteine proteases in the ubiquitin pathway.
  EMBO Rep, 4, 517-522.  
14517261 P.Y.Wu, M.Hanlon, M.Eddins, C.Tsui, R.S.Rogers, J.P.Jensen, M.J.Matunis, A.M.Weissman, A.M.Weisman, A.M.Weissman, C.Wolberger, C.P.Wolberger, and C.M.Pickart (2003).
A conserved catalytic residue in the ubiquitin-conjugating enzyme family.
  EMBO J, 22, 5241-5250.  
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Deubiquitinating enzymes--the importance of driving in reverse along the ubiquitin-proteasome pathway.
  Int J Biochem Cell Biol, 35, 590-605.  
12759362 T.Gan-Erdene, K.Nagamalleswari, L.Yin, K.Wu, Z.Q.Pan, and K.D.Wilkinson (2003).
Identification and characterization of DEN1, a deneddylase of the ULP family.
  J Biol Chem, 278, 28892-28900.  
14522054 Y.Liu, H.A.Lashuel, S.Choi, X.Xing, A.Case, J.Ni, L.A.Yeh, G.D.Cuny, R.L.Stein, and P.T.Lansbury (2003).
Discovery of inhibitors that elucidate the role of UCH-L1 activity in the H1299 lung cancer cell line.
  Chem Biol, 10, 837-846.  
12507430 M.Hu, P.Li, M.Li, W.Li, T.Yao, J.W.Wu, W.Gu, R.E.Cohen, and Y.Shi (2002).
Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.
  Cell, 111, 1041-1054.
PDB codes: 1nb8 1nbf
12021365 M.Y.Balakirev, M.Jaquinod, A.L.Haas, and J.Chroboczek (2002).
Deubiquitinating function of adenovirus proteinase.
  J Virol, 76, 6323-6331.  
12408865 Y.Liu, L.Fallon, H.A.Lashuel, Z.Liu, and P.T.Lansbury (2002).
The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson's disease susceptibility.
  Cell, 111, 209-218.  
11473704 C.Ingvardsen, and B.Veierskov (2001).
Ubiquitin- and proteasome-dependent proteolysis in plants.
  Physiol Plant, 112, 451-459.  
11395416 C.M.Pickart (2001).
Mechanisms underlying ubiquitination.
  Annu Rev Biochem, 70, 503-533.  
10882122 E.Mossessova, and C.D.Lima (2000).
Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast.
  Mol Cell, 5, 865-876.
PDB code: 1euv
10938131 H.Lin, A.Keriel, C.R.Morales, N.Bedard, Q.Zhao, P.Hingamp, S.Lefrançois, L.Combaret, and S.S.Wing (2000).
Divergent N-terminal sequences target an inducible testis deubiquitinating enzyme to distinct subcellular structures.
  Mol Cell Biol, 20, 6568-6578.  
10906270 K.D.Wilkinson (2000).
Ubiquitination and deubiquitination: targeting of proteins for degradation by the proteasome.
  Semin Cell Dev Biol, 11, 141-148.  
10558980 L.Huang, E.Kinnucan, G.Wang, S.Beaudenon, P.M.Howley, J.M.Huibregtse, and N.P.Pavletich (1999).
Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade.
  Science, 286, 1321-1326.
PDB codes: 1c4z 1d5f
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.