PDBsum entry 1uch

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Cysteine protease PDB id
Protein chain
206 a.a. *
Waters ×104
* Residue conservation analysis
PDB id:
Name: Cysteine protease
Title: Deubiquitinating enzyme uch-l3 (human) at 1.8 angstrom resolution
Structure: Ubiquitin c-terminal hydrolase uch-l3. Chain: a. Synonym: uch-l3,dub. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell_line: b834 (de3). Tissue: hematopoetic. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: gal-met- auxotroph.
1.80Å     R-factor:   0.232     R-free:   0.294
Authors: S.C.Johnston,C.N.Larsen,W.J.Cook,K.D.Wilkinson,C.P.Hill
Key ref:
S.C.Johnston et al. (1997). Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO J, 16, 3787-3796. PubMed id: 9233788 DOI: 10.1093/emboj/16.13.3787
06-Oct-97     Release date:   28-Jan-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P15374  (UCHL3_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase isozyme L3
230 a.a.
206 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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     intracellular   4 terms 
  Biological process     protein catabolic process   3 terms 
  Biochemical function     protein binding     7 terms  


DOI no: 10.1093/emboj/16.13.3787 EMBO J 16:3787-3796 (1997)
PubMed id: 9233788  
Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution.
S.C.Johnston, C.N.Larsen, W.J.Cook, K.D.Wilkinson, C.P.Hill.
Ubiquitin C-terminal hydrolases catalyze the removal of adducts from the C-terminus of ubiquitin. We have determined the crystal structure of the recombinant human Ubiquitin C-terminal Hydrolase (UCH-L3) by X-ray crystallography at 1.8 A resolution. The structure is comprised of a central antiparallel beta-sheet flanked on both sides by alpha-helices. The beta-sheet and one of the helices resemble the well-known papain-like cysteine proteases, with the greatest similarity to cathepsin B. This similarity includes the UCH-L3 active site catalytic triad of Cys95, His169 and Asp184, and the oxyanion hole residue Gln89. Papain and UCH-L3 differ, however, in strand and helix connectivity, which in the UCH-L3 structure includes a disordered 20 residue loop (residues 147-166) that is positioned over the active site and may function in the definition of substrate specificity. Based upon analogy with inhibitor complexes of the papain-like enzymes, we propose a model describing the binding of ubiquitin to UCH-L3. The UCH-L3 active site cleft appears to be masked in the unliganded structure by two different segments of the enzyme (residues 9-12 and 90-94), thus implying a conformational change upon substrate binding and suggesting a mechanism to limit non-specific hydrolysis.
  Selected figure(s)  
Figure 4.
Figure 4 Comparison of UCH-L3 and papain-like active sites. Active site residues of UCH-L3. Gln89, Cys95, His169 and Asp184 are shown with thick lines. A representative collection of eight papain-like enzyme active sites is shown by thin lines following least-squares overlap on the active site residue C^ atoms. The papain-like structures shown have PDB identifiers 9pap, 4pad, 1pop, 2act, 1aec, 1huc, 1csb and 1gec. Other papain-like structures used in structural comparisons in this paper are: 1the, 1cpj, 1pad, 2pad, 5pad, 6pad, 1stf, 1pip, 1ppp, 1pe6, 1ppd, 1ppn and 1ppo. Refer to the PDB for primary references to these structures, which are not included here because of space limits.
Figure 6.
Figure 6 Active site clefts of papain-like enzymes and UCH-L3. Orientation is the same as for Figure 3. (A) Glycyl endopeptidase complex with the inhibitor benzyloxycarbonyl-L-V-G-methylene, which occupies the S4, S3, S2 and S1 sites (O'Hara et al., 1995). (B) Cathepsin B with the inhibitor CA030, which occupies the S2, S1, S1' and S2' sites (Turk et al., 1995). Protein surfaces are colored gray/green according to curvature. Bound inhibitors are red. The active site Cys residue is yellow, other active site residues are magenta. (C) UCH-L3 molecular surface colored for the invariant residues of Figure 1. Active site residues are shown in magenta, basic residues blue, acidic residues red, polar residues cyan and hydrophobic residues green. This figure was prepared with the program GRASP (Nicholls et al., 1991).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 3787-3796) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20439756 D.A.Boudreaux, T.K.Maiti, C.W.Davies, and C.Das (2010).
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
20012716 F.I.Andersson, S.E.Jackson, and S.T.Hsu (2010).
Backbone assignments of the 26 kDa neuron-specific ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1).
  Biomol NMR Assign, 4, 41-43.  
19879917 I.N.Day, and R.J.Thompson (2010).
UCHL1 (PGP 9.5): neuronal biomarker and ubiquitin system protein.
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Connecting the Dots: Interplay Between Ubiquitylation and SUMOylation at DNA Double Strand Breaks.
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20436459 J.C.Scheuermann, Ayala Alonso, K.Oktaba, N.Ly-Hartig, R.K.McGinty, S.Fraterman, M.Wilm, T.W.Muir, and J.Müller (2010).
Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB.
  Nature, 465, 243-247.  
20042598 K.Artavanis-Tsakonas, W.A.Weihofen, J.M.Antos, B.I.Coleman, C.A.Comeaux, M.T.Duraisingh, R.Gaudet, and H.L.Ploegh (2010).
Characterization and structural studies of the Plasmodium falciparum ubiquitin and Nedd8 hydrolase UCHL3.
  J Biol Chem, 285, 6857-6866.
PDB codes: 2wdt 2we6
19626045 D.Komander, M.J.Clague, and S.Urbé (2009).
Breaking the chains: structure and function of the deubiquitinases.
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19086784 D.Majumdar, M.D.Alexander, and J.K.Coward (2009).
Synthesis of isopeptide epoxide peptidomimetics.
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19243136 F.E.Reyes-Turcu, and K.D.Wilkinson (2009).
Polyubiquitin binding and disassembly by deubiquitinating enzymes.
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19489724 F.E.Reyes-Turcu, K.H.Ventii, and K.D.Wilkinson (2009).
Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes.
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19282967 J.H.Fong, B.A.Shoemaker, S.O.Garbuzynskiy, M.Y.Lobanov, O.V.Galzitskaya, and A.R.Panchenko (2009).
Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis.
  PLoS Comput Biol, 5, e1000316.  
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.
  J Biol Chem, 284, 3593-3602.  
19188440 S.Misaghi, S.Ottosen, A.Izrael-Tomasevic, D.Arnott, M.Lamkanfi, J.Lee, J.Liu, K.O'Rourke, V.M.Dixit, and A.C.Wilson (2009).
Association of C-terminal ubiquitin hydrolase BRCA1-associated protein 1 with cell cycle regulator host cell factor 1.
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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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18321862 B.H.Ha, H.C.Ahn, S.H.Kang, K.Tanaka, C.H.Chung, and E.E.Kim (2008).
Structural basis for Ufm1 processing by UfSP1.
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18601651 M.Drag, J.Mikolajczyk, M.Bekes, F.E.Reyes-Turcu, J.A.Ellman, K.D.Wilkinson, and G.S.Salvesen (2008).
Positional-scanning fluorigenic substrate libraries reveal unexpected specificity determinants of DUBs (deubiquitinating enzymes).
  Biochem J, 415, 367-375.  
18307031 Q.Wang, Y.Liu, X.Zou, Q.Wang, M.An, X.Guan, J.He, Y.Tong, and J.Ji (2008).
The hippocampal proteomic analysis of senescence-accelerated mouse: implications of Uchl3 and mitofilin in cognitive disorder and mitochondria dysfunction in SAMP8.
  Neurochem Res, 33, 1776-1782.  
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).
Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex.
  Mol Cell, 31, 909-917.  
18485060 Y.Liu, F.Wang, H.Zhang, H.He, L.Ma, and X.W.Deng (2008).
Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development.
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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
17948018 K.R.Love, A.Catic, C.Schlieker, and H.L.Ploegh (2007).
Mechanisms, biology and inhibitors of deubiquitinating enzymes.
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17610893 M.May, S.Mehboob, D.C.Mulhearn, Z.Wang, H.Yu, G.R.Thatcher, B.D.Santarsiero, M.E.Johnson, and A.D.Mesecar (2007).
Structural and functional analysis of two glutamate racemase isozymes from Bacillus anthracis and implications for inhibitor design.
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PDB codes: 2dwu 2gzm
  20103862 Y.Chen (2007).
The enzymes in ubiquitin-like post-translational modifications.
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16608434 B.M.Kessler (2006).
Putting proteomics on target: activity-based profiling of ubiquitin and ubiquitin-like processing enzymes.
  Expert Rev Proteomics, 3, 213-221.  
16537382 C.Das, Q.Q.Hoang, C.A.Kreinbring, S.J.Luchansky, R.K.Meray, S.S.Ray, P.T.Lansbury, D.Ringe, and G.A.Petsko (2006).
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
17035239 G.V.Avvakumov, J.R.Walker, S.Xue, P.J.Finerty, F.Mackenzie, E.M.Newman, and S.Dhe-Paganon (2006).
Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8).
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PDB codes: 2a9u 2fzp 2gfo 2gwf
16287140 J.Bielnicki, Y.Devedjiev, U.Derewenda, Z.Dauter, A.Joachimiak, and Z.S.Derewenda (2006).
B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.
  Proteins, 62, 144-151.
PDB code: 1y7m
16925553 K.Artavanis-Tsakonas, S.Misaghi, C.A.Comeaux, A.Catic, E.Spooner, M.T.Duraisingh, and H.L.Ploegh (2006).
Identification by functional proteomics of a deubiquitinating/deNeddylating enzyme in Plasmodium falciparum.
  Mol Microbiol, 61, 1187-1195.  
16581910 K.Ratia, K.S.Saikatendu, B.D.Santarsiero, N.Barretto, S.C.Baker, R.C.Stevens, and A.D.Mesecar (2006).
Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme.
  Proc Natl Acad Sci U S A, 103, 5717-5722.
PDB code: 2fe8
16905103 M.Renatus, S.G.Parrado, A.D'Arcy, U.Eidhoff, B.Gerhartz, U.Hassiepen, B.Pierrat, R.Riedl, D.Vinzenz, S.Worpenberg, and M.Kroemer (2006).
Structural basis of ubiquitin recognition by the deubiquitinating protease USP2.
  Structure, 14, 1293-1302.
PDB code: 2hd5
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.  
15651044 A.Borodovsky, H.Ovaa, W.J.Meester, E.S.Venanzi, M.S.Bogyo, B.G.Hekking, H.L.Ploegh, B.M.Kessler, and H.S.Overkleeft (2005).
Small-molecule inhibitors and probes for ubiquitin- and ubiquitin-like-specific proteases.
  Chembiochem, 6, 287-291.  
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
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.
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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
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.
  J Virol, 79, 15189-15198.  
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
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.
  Structure, 12, 1519-1531.
PDB codes: 1tgz 1th0
15265035 M.Albrecht, M.Golatta, U.Wüllner, and T.Lengauer (2004).
Structural and functional analysis of ataxin-2 and ataxin-3.
  Eur J Biochem, 271, 3155-3170.  
15258613 M.H.Nanao, S.O.Tcherniuk, J.Chroboczek, O.Dideberg, A.Dessen, and M.Y.Balakirev (2004).
Crystal structure of human otubain 2.
  EMBO Rep, 5, 783-788.
PDB code: 1tff
14694194 M.Zhu, F.Shao, R.W.Innes, J.E.Dixon, and Z.Xu (2004).
The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site.
  Proc Natl Acad Sci U S A, 101, 302-307.
PDB code: 1ukf
15242591 R.Zhang, R.Wu, G.Joachimiak, S.K.Mazmanian, D.M.Missiakas, P.Gornicki, O.Schneewind, and A.Joachimiak (2004).
Structures of sortase B from Staphylococcus aureus and Bacillus anthracis reveal catalytic amino acid triad in the active site.
  Structure, 12, 1147-1156.
PDB codes: 1ng5 1rz2
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.  
12488316 B.Kessler, X.Hong, J.Petrovic, A.Borodovsky, N.P.Dantuma, M.Bogyo, H.S.Overkleeft, H.Ploegh, and R.Glas (2003).
Pathways accessory to proteasomal proteolysis are less efficient in major histocompatibility complex class I antigen production.
  J Biol Chem, 278, 10013-10021.  
12759363 K.Wu, K.Yamoah, G.Dolios, T.Gan-Erdene, P.Tan, A.Chen, C.G.Lee, N.Wei, K.D.Wilkinson, R.Wang, and Z.Q.Pan (2003).
DEN1 is a dual function protease capable of processing the C terminus of Nedd8 and deconjugating hyper-neddylated CUL1.
  J Biol Chem, 278, 28882-28891.  
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.  
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.  
12672452 S.S.Wing (2003).
Deubiquitinating enzymes--the importance of driving in reverse along the ubiquitin-proteasome pathway.
  Int J Biochem Cell Biol, 35, 590-605.  
12711609 S.Shin, Y.S.Yun, H.M.Koo, Y.S.Kim, K.Y.Choi, and B.H.Oh (2003).
Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad.
  J Biol Chem, 278, 24937-24943.
PDB codes: 1o9n 1o9o 1o9p 1o9q 1obi 1obj 1obk 1obl 1och 1ock 1ocl 1ocm
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.  
11864977 Y.Wang, and H.G.Dohlman (2002).
Pheromone-dependent ubiquitination of the mitogen-activated protein kinase kinase Ste7.
  J Biol Chem, 277, 15766-15772.  
11076031 A.Y.Amerik, S.J.Li, and M.Hochstrasser (2000).
Analysis of the deubiquitinating enzymes of the yeast Saccharomyces cerevisiae.
  Biol Chem, 381, 981-992.  
11018721 C.A.Gilchrist, and R.T.Baker (2000).
Characterization of the ubiquitin-specific protease activity of the mouse/human Unp/Unph oncoprotein.
  Biochim Biophys Acta, 1481, 297-309.  
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.
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10713173 L.J.Kurihara, E.Semenova, J.M.Levorse, and S.M.Tilghman (2000).
Expression and functional analysis of Uch-L3 during mouse development.
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10320326 A.L.Lamb, and M.E.Newcomer (1999).
The structure of retinal dehydrogenase type II at 2.7 A resolution: implications for retinal specificity.
  Biochemistry, 38, 6003-6011.
PDB code: 1bi9
10073263 A.L.Schwartz, and A.Ciechanover (1999).
The ubiquitin-proteasome pathway and pathogenesis of human diseases.
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10872471 D.Voges, P.Zwickl, and W.Baumeister (1999).
The 26S proteasome: a molecular machine designed for controlled proteolysis.
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Ubiquitin binding interface mapping on yeast ubiquitin hydrolase by NMR chemical shift perturbation.
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The ubiquitin system.
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Substrate specificity of deubiquitinating enzymes: ubiquitin C-terminal hydrolases.
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Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes.
  J Biol Chem, 273, 34983-34991.
PDB code: 1ndd
9564029 F.G.Whitby, J.D.Phillips, J.P.Kushner, and C.P.Hill (1998).
Crystal structure of human uroporphyrinogen decarboxylase.
  EMBO J, 17, 2463-2471.
PDB code: 1uro
9485312 L.C.Dang, F.D.Melandri, and R.L.Stein (1998).
Kinetic and mechanistic studies on the hydrolysis of ubiquitin C-terminal 7-amido-4-methylcoumarin by deubiquitinating enzymes.
  Biochemistry, 37, 1868-1879.  
9632704 S.Halfon, J.Ford, J.Foster, L.Dowling, L.Lucian, M.Sterling, Y.Xu, M.Weiss, M.Ikeda, D.Liggett, A.Helms, C.Caux, S.Lebecque, C.Hannum, S.Menon, T.McClanahan, D.Gorman, and G.Zurawski (1998).
Leukocystatin, a new Class II cystatin expressed selectively by hematopoietic cells.
  J Biol Chem, 273, 16400-16408.  
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.