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Thioesterase

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<StructureSection load='2hd5' size='450' side='right' caption='Human ubiquitin esterase 2 (deepskyblue) complex with ubiquitin (green) and zinc+2 ion (grey) (PDB code [[2hd5]]).' scene='48/489265/Cv/2'>
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<StructureSection load='' size='350' side='right' caption='Human ubiquitin esterase 2 (deepskyblue) complex with ubiquitin (green) and zinc+2 ion (grey) (PDB code [[2hd5]]).' scene='48/489265/Cv/2'>
__TOC__
__TOC__
== Function ==
== Function ==
Line 28: Line 28:
== Structural highlights ==
== Structural highlights ==
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<scene name='48/489265/Cv/4'>Human ubiquitin esterase 2 complex with ubiquitin and zinc+2 ion</scene>. Ubiquitin thioesterase 2 active site contains the <scene name='48/489265/Cv/1'>catalytic triad Cys-His-Asn and the oxyanion hole Asn</scene>. The metal-binding enzyme contains a Zn+2 ion which coordinates to 4 Cys residues. The ubiquitin coordinates to the thioesterase via residues in all thioesterase domains: finger, palm and thumb<ref>PMID:16905103</ref>.
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<scene name='48/489265/Cv/7'>Human ubiquitin esterase 2 complex with ubiquitin and zinc+2 ion</scene>. Ubiquitin thioesterase 2 active site contains the <scene name='48/489265/Cv/8'>catalytic triad Cys-His-Asn and the oxyanion hole Asn</scene>. The metal-binding enzyme contains a <scene name='48/489265/Cv/9'>Zn+2 ion which coordinates to 4 Cys residues</scene>. The <scene name='48/489265/Cv/10'>ubiquitin coordinates to the thioesterase via residues in all thioesterase domains: finger, palm and thumb</scene><ref>PMID:16905103</ref>.
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</StructureSection>
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==3D structures of thioesterase==
==3D structures of thioesterase==
 +
[[Thioesterase 3D structures]]
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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</StructureSection>
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Maristoyl-ACP-specific thioesterase
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**[[1tht]] – TE – ''Vibrio harveyi''
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-
 
+
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*4-hydroxybenzoyl-CoA thioesterase
+
-
 
+
-
**[[1bvq]] – PsTE – ''Pseudomonas''<br />
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**[[1lo7]] – PsTE + 4-hydroxyphenyl CoA<br />
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**[[1lo9]] - PsTE (mutant) + 4-hydroxybenzoyl CoA<br />
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**[[1lo8]] - PsTE + 4-hydroxybenzyl CoA<br />
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**[[1q4s]] - ArTE + 4-hydroxybenzoate – '''Arthrobacte''r'<br />
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**[[1q4t]] - ArTE + 4-hydroxyphenyl CoA<br />
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**[[1q4u]] - ArTE + 4-hydroxybenzyl CoA<br />
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**[[3r32]], [[3r35]], [[3r37]], [[3r38]], [[3r3b]], [[3r3c]], [[3r3d]], [[3r3f]], [[3tea]] - ArTE (mutant) + 4-hydroxyphenacyl CoA<br />
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**[[3r36]] - ArTE (mutant) + 4-hydroxybenzoate<br />
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**[[3r3a]] - ArTE (mutant) + 4-hydroxybenzoate + CoA<br />
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**[[3r34]] - ArTE (mutant) + CoA<br />
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-
 
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*Palmitoyl protein thioesterase
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**[[1eh5]] – bTE1 + Palmitate – bovine<br />
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**[[1ei9]] – bTE1<br />
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**[[1exw]] – bTE1 + hexadecylsulfonyl fluoride<br />
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**[[1pja]] – hTEII – human<br />
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**[[3gro]] - hTEI
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+
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*Acyl-CoA thioesterase
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+
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**[[1c8u]] – EcTEII – ''Escherichia coli''<br />
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**[[1ivn]] – EcTEI<br />
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**[[1jrl]] – EcTEI (mutant) <br />
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**[[1j00]] – EcTEI + diethyl phosphono derivative<br />
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**[[1v2g]], [[1u8u]] - EcTEI + octanoic acid<br />
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**[[2v1o]] – mTE7 hotdog domain – mouse<br />
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**[[2q2b]] – mTE7 C terminal<br />
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**[[2pzh]] - TE - ''Helicobacter pylori''<br />
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**[[3hlk]] – hTE2<br />
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**[[3k2i]] – hTE4<br />
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**[[2qq2]] - hTE7 C terminal<br />
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**[[3fo5]] – hTE11 START domain<br />
+
-
**[[3b7k]], [[4moc]] – hTE12<br />
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**[[4mob]] – hTE12 + ADP<br />
+
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**[[3rd7]] – TE – ''Mycobacterium avium''<br />
+
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**[[3u0a]] – TEII – ''Mycobacterium marinum''<br />
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**[[1tbu]] – TE N terminal (peroximal) – yeast<br />
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**[[4qfw]] – YpTE II – ''Yersinia pestis''<br />
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**[[4r4u]] – YpTE II + CoA<br />
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**[[5t02]] – TE (mutant) + CoA + GDP – ''Neisseria meningitis''<br />
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**[[5hz4]], [[5hwf]], [[5egk]] – SaTE (mutant) – ''Staphylococcus aureus''<br />
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**[[4egj]] – SaTE + CoA<br />
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*Acyl protein thioesterase
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+
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**[[1fj2]] – EcTEI
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*Acyl-ACP thioesterase
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+
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**[[2ess]] – TE – ''Bacterioides thetaiotaomicron''<br />
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**[[4gak]] – TE – ''Spirosoma linguale''<br />
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**[[4gwh]] – YpTE <br />
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*ACP-polyene thioesterase
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+
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**[[4i4j]] – TE – ''Streptomyces globisporus''<br />
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+
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*Fluoroacetyl-CoA thioesterase
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+
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**[[3kuv]], [[3kuw]], [[3kvi]] – ScTE (mutant) + acetate derivative – ''Streptomyces cattleya''<br />
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**[[3kv7]], [[3kv8]], [[3p2r]], [[3p2s]] – ScTE + acetate derivative<br />
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**[[3kvu]] – ScTE + acetyl-CoA<br />
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**[[3kvz]], [[3kw1]] – ScTE + FAcOPan<br />
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**[[3kx7]], [[3kx8]], [[3p2q]] – ScTE <br />
+
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**[[3p3f]] – ScTE (mutant) <br />
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**[[3p3i]] - ScTE (mutant) + acetate derivative + CoA<br />
+
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+
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*Dihydroxynaphthoyl-CoA thioesterase
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+
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**[[4k00]] – TE – ''Synechocystis''<br />
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**[[4k02]] – AtTE – ''Arabidopsis thaliana''<br />
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-
 
+
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*RedJ thioesterase
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+
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**[[3qmv]], [[3qmw]] – TE –'' Streptomyces coelicolor''
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-
 
+
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*Orf6 thioesterase
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+
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**[[4i45]] – TE – ''Photobacterium profundum''<br />
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+
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*thioesterase
+
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+
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**[[2av9]], [[2o5u]], [[2o6b]], [[2o6t]], [[2o6u]], [[3qy3]] – TE – ''Pseudomonas aeruginosa''
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+
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*Ubiquitin thioesterase
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+
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*Ubiquitin thioesterase 2
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+
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**[[2zfy]] – hUSP – human <BR />
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**[[2hd5]], [[3nhe]], [[3v6c]], [[3v6e]] – hUSP + Ub <BR />
+
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**[[1tff]] – hUSP (mutant) <BR />
+
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**[[2ibi]] – hUSP (mutant) + Ub <BR />
+
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+
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*Ubiquitin thioesterase 3
+
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+
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**[[2qiy]] – yUSP + USP-associated protein – yeast <BR />
+
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+
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*Ubiquitin thioesterase 4
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+
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**[[2y6e]] – hUSP catalytic domain <br />
+
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**[[3jyu]] – mUSP N terminal domain - mouse<br />
+
-
 
+
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*Ubiquitin thioesterase 5
+
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+
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**[[2dag]] – hUSP UBA domain 1 - NMR<br />
+
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**[[2dak]] – hUSP UBA domain 2 - NMR<br />
+
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**[[2g43]] – hUSP zinc finger USP domain<br />
+
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**[[2g45]] – hUSP zinc finger USP domain + Ub<br />
+
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**[[3ihp]] – hUSP + Ub <BR />
+
-
 
+
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*Ubiquitin thioesterase 7
+
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+
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**[[2f1z]], [[5j7t]] – hUSP<br />
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-
**[[1nb8]], [[4m5w]], [[4m5x]] – hUSP catalytic domain <br />
+
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**[[2kvr]] – hUSP UBL domain - NMR<br />
+
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**[[4pyz]], [[4wph]], [[4wpi]] – hUSP UBL domains 1+2<br />
+
-
5fwi]] – hUSP catalytic + UBL domains 1+2<br />
+
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**[[1yze]], [[2f1w]] – hUSP N terminal domain <br />
+
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**[[2ylm]] – hUSP C terminal domain <br />
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**[[2f1x]], [[2f1y]], [[2foj]], [[2foo]], [[2fop]] – hUSP N terminal domain/peptide <br />
+
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**[[4zv3]] – mUSP N terminal domain <br />
+
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+
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*Ubiquitin thioesterase 7 complexes
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+
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**[[1nbf]] – hUSP catalytic domain + Ub aldehyde<br />
+
-
**[[5jtj]] – hUSP catalytic domain + Ub <br />
+
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**[[1yy6]] – hUSP N terminal domain + EBNA1 peptide<br />
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**[[2xxn]] – hUSP TRAF domain + VIRF-4 peptide<br />
+
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**[[3mqr]] – hUSP TRAF domain + HDMX peptide<br />
+
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**[[3mqs]] – hUSP TRAF domain + HDM2 peptide<br />
+
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**[[4jjq]] – hUSP TRAF domain + E2 peptide<br />
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**[[4kg9]] – hUSP TRAF domain + MCM-BP peptide<br />
+
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**[[4ysi]] – hUSP TRAF domain + peptide<br />
+
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**[[4yoc]] – hUSP residues 560-1102 + DNA methyl transferase<br />
+
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**[[5c6d]] – hUSP residues 561-881 + UHRF1<br />
+
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**[[5c56]] – hUSP residues 560-1102 + Ub E3 ligase Icp0444w<br />
+
-
 
+
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*Ubiquitin thioesterase 8
+
-
 
+
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**[[1whb]] – hUSP rhodanase domain - NMR<br />
+
-
**[[2a9u]] – hUSP N terminal domain <br />
+
-
**[[2gfo]] – hUSP catalytic domain <br />
+
-
 
+
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*Ubiquitin thioesterase 8 complexes
+
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+
-
**[[2gwf]] – hUSP rhodanase domain + ring finger protein 41 USP8 interaction domain<br />
+
-
**[[3mhh]], [[3m99]], [[4fip]], [[4fjc]], [[4f5k]], [[4fk5]] – yUSP + SUS1 + SGF11 +SGF73 <br />
+
-
**[[3mhs]] – yUSP + SUS1 + SGF11 +SGF73 + Ub<br />
+
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**[[4zux]] – yUSP + SUS1 + SGF11 +SGF73 + Ub + Histones H3,2, H4, H2A, H2B + DNA<br />
+
-
**[[3n3k]] – hUSP catalytic domain + Ub<br />
+
-
 
+
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*Ubiquitin thioesterase 11
+
-
 
+
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**[[4mel]] – hUSP DUSP+UBL domains <br />
+
-
**[[4mem]] – rUSP DUSP+UBL domains - rat<br />
+
-
 
+
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*Ubiquitin thioesterase 12
+
-
 
+
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**[[5k16]] – hUSP <br />
+
-
**[[5k1a]], [[5k1b]], [[5k1c]] – hUSP + WD repeat-containing protein<br />
+
-
 
+
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*Ubiquitin thioesterase 13
+
-
 
+
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**[[2l80]] – hUSP zinc finger domain - NMR<br />
+
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**[[2lbc]] – hUSP UBA domain - NMR<br />
+
-
 
+
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*Ubiquitin thioesterase 14
+
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+
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**[[1wgg]] – mUSP N terminal domain - NMR<br />
+
-
**[[2ayn]] – hUSP<br />
+
-
**[[2ayo]] – hUSP + Ub aldehyde<br />
+
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**[[1wiv]] – AtUSP UBA domain - NMR<br />
+
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**[[5gjq]] – hUSP in proteasome – Cryo EM<br />
+
-
 
+
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*Ubiquitin thioesterase 15
+
-
 
+
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**[[3lmn]] – hUSP DUSP domain <BR />
+
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**[[3ppa]], [[3pv1]], [[3t9l]], [[4a3o]], [[4a3p]] – hUSP DUSP+UBL domains <br />
+
-
**[[1w6v]] – hUSP DUSP domain - NMR<br />
+
-
**[[5jjw]] – hUSP catalytic domain + SART HAT domain<br />
+
-
**[[5ctr]] – hUSP DUSP+UBL domains + SART HAT domain <br />
+
-
 
+
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*Ubiquitin thioesterase 16
+
-
 
+
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**[[2i50]] – hUSP zinc finger domain - NMR <BR />
+
-
 
+
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*Ubiquitin thioesterase 18
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+
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**[[5cht]] – hUSP <BR />
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-
 
+
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*Ubiquitin thioesterase 21
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+
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**[[3i3t]], [[2y5b]] – hUSP + Ub <BR />
+
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**[[3mtn]] – hUSP + Ub inhibitor <BR />
+
-
 
+
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*Ubiquitin thioesterase 25
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+
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**[[1vdl]] – mUSP catalytic domain <br />
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+
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*Ubiquitin thioesterase 28
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+
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**[[2lva]], [[2muu]], [[2mux]] – hUSP N terminal - NMR <BR />
+
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+
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*Ubiquitin thioesterase 33
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+
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**[[2uzg]] – hUSP zinc finger domain - NMR <BR />
+
-
 
+
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*Ubiquitin thioesterase 37
+
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+
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**[[3ihr]] – hUSP (mutant) <BR />
+
-
**[[3a7s]] – hUSP catalytic domain (mutant) <BR />
+
-
**[[3u12]] – hUSP pleckstrin domain <br />
+
-
 
+
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*Ubiquitin thioesterase 38
+
-
 
+
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**[[4rxx]] – hUSP N terminal <BR />
+
-
 
+
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*Ubiquitin thioesterase 46
+
-
 
+
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**[[5cvm]] – hUSP + Ub <BR />
+
-
**[[5cvn]], [[5cvo]] – hUSP + WD repeat-containing protein + Ub<br />
+
-
 
+
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*Ubiquitin thioesterase Cyld
+
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+
-
**[[2vhf]] – hUSP USP domain <BR />
+
-
 
+
-
*Ubiquitin thioesterase L1
+
-
 
+
-
**[[2etl]] – hUSP-L1 <br />
+
-
**[[3irt]], [[4jkj]] – hUSP (mutant) <BR />
+
-
**[[2len]] – hUSP (mutant) - NMR<BR />
+
-
**[[3ifw]], [[3kvf]], [[3kw5]] – hUSP (mutant) + Ub<BR />
+
-
**[[4dm9]] – hUSP + peptide inhibitor<BR />
+
-
 
+
-
*Ubiquitin thioesterase L3
+
-
 
+
-
**[[1uch]] – hUSP-L3 <br />
+
-
**[[1xd3]] – hUSP-L3 + UBC<br />
+
-
**[[2we6]] – PfUSP-L3 – ''Plasmodium falciparum''<br />
+
-
**[[2wdt]] – PfUSP-L3 + Ub <br />
+
-
 
+
-
*Ubiquitin thioesterase L5
+
-
 
+
-
**[[3ris]] – hUSP catalytic domain <BR />
+
-
**[[3rii]], [[3a7s]] – hUSP catalytic domain (mutant) <BR />
+
-
**[[3tb3]] – hUSP UCH domain (mutant) <BR />
+
-
**[[3ihr]] – hUSP-L5 (mutant) <br />
+
-
**[[4uel]] – hUSP-L5 + polyUb + proteasomal Ub receptor Deubad domain <br />
+
-
**[[4uem]] – hUSP-L5 + proteasomal Ub receptor Deubad domain <br />
+
-
**[[4wlq]] – mUSP-L5 + proteasomal Ub receptor C terminal <br />
+
-
**[[4wlr]] – mUSP-L5 + polyUb + proteasomal Ub receptor C terminal <br />
+
-
**[[4uf5]], [[4wlp]] – hUSP-L5 + nuclear factor Deubad domain <br />
+
-
**[[4uf6]] – hUSP-L5 + polyUb + nuclear factor Deubad domain <br />
+
-
 
+
-
*Ubiquitin thioesterase ZranB1
+
-
 
+
-
**[[3zrh]] – hUSP <BR />
+
-
**[[4s1z]] – bUSP zinc finger + Ub <BR />
+
-
 
+
-
*Ubiquitin thioesterase OTUB1
+
-
 
+
-
**[[3von]] – hUSP + E2 <BR />
+
-
**[[4ddg]], [[4ddi]] – hUSP + Ub<BR />
+
-
**[[4i6l]] – hUSP (mutant) + Ub<BR />
+
-
**[[4dhz]], [[4ldt]] – hUSP + E2 + Ub<BR />
+
-
**[[4boq]] - hUSP OTU domain <BR />
+
-
**[[4boz]] - hUSP OTU domain (mutant) + Ub <BR />
+
-
**[[4bos]] - hUSP OTU domain (mutant) + Ub + OTUD2 peptide<BR />
+
-
**[[4fjv]] - hUSP OTUB2 + Ub <BR />
+
-
**[[4dhj]] – nUSP + E2 + Ub - nematode<BR />
+
-
**[[4dhi]] – nUSP + E2 <BR />
+
-
**[[2kzr]] – mUSP UBX-like domain – NMR<br />
+
-
**[[4kdi]], [[4kdl]] – yUSP UBX-like domain + transitional endoplasmic reticulum ATPase<br />
+
-
**[[3by4]], [[3c0r]] - yUSP OTU domain + Ub<BR />
+
-
 
+
-
*Ubiquitin thioesterase
+
-
 
+
-
**[[3znh]] – USP OTU domain + Ub – Crimean-Congo hemorrhagic fever virus<BR />
+
-
 
+
-
*Pseudomonas aeruginosa TE
+
-
 
+
-
**[[2av9]], [[2o5u]], [[2o6b]], [[2o6t]], [[2o6u]], [[3qy3]] – PaTE – ''Pseudomonas aeruginosa''<br />
+
-
**[[4qd7]] – PaTE hotdog domain<br />
+
-
**[[4qda]], [[4qdb]] – PaTE hotdog domain (mutant)<br />
+
-
**[[4qd8]], [[4dq9]] – PaTE hotdog domain + acyl-CoA derivatives<br />
+
-
 
+
-
}}
 
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Human ubiquitin esterase 2 (deepskyblue) complex with ubiquitin (green) and zinc+2 ion (grey) (PDB code 2hd5).

Drag the structure with the mouse to rotate

References

  1. ↑ Cho S, Dawson G. Palmitoyl protein thioesterase 1 protects against apoptosis mediated by Ras-Akt-caspase pathway in neuroblastoma cells. J Neurochem. 2000 Apr;74(4):1478-88. PMID:10737604
  2. ↑ Zhuang Z, Gartemann KH, Eichenlaub R, Dunaway-Mariano D. Characterization of the 4-hydroxybenzoyl-coenzyme A thioesterase from Arthrobacter sp. strain SU. Appl Environ Microbiol. 2003 May;69(5):2707-11. PMID:12732540
  3. ↑ Hunt MC, Alexson SE. The role Acyl-CoA thioesterases play in mediating intracellular lipid metabolism. Prog Lipid Res. 2002 Mar;41(2):99-130. PMID:11755680
  4. ↑ Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC. Structural and Biochemical Studies of a Fluoroacetyl-CoA-Specific Thioesterase Reveal a Molecular Basis for Fluorine Selectivity. Biochemistry. 2010 Oct 11. PMID:20836570 doi:10.1021/bi101102u
  5. ↑ Jagannathan M, Nguyen T, Gallo D, Luthra N, Brown GW, Saridakis V, Frappier L. A role for USP7 in DNA replication. Mol Cell Biol. 2014 Jan;34(1):132-45. doi: 10.1128/MCB.00639-13. Epub 2013 Nov 4. PMID:24190967 doi:http://dx.doi.org/10.1128/MCB.00639-13
  6. ↑ Jahan AS, Lestra M, Swee LK, Fan Y, Lamers MM, Tafesse FG, Theile CS, Spooner E, Bruzzone R, Ploegh HL, Sanyal S. Usp12 stabilizes the T-cell receptor complex at the cell surface during signaling. Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E705-14. doi:, 10.1073/pnas.1521763113. Epub 2016 Jan 25. PMID:26811477 doi:http://dx.doi.org/10.1073/pnas.1521763113
  7. ↑ Malhotra S, Morcillo-Suarez C, Nurtdinov R, Rio J, Sarro E, Moreno M, Castillo J, Navarro A, Montalban X, Comabella M. Roles of the ubiquitin peptidase USP18 in multiple sclerosis and the response to interferon-beta treatment. Eur J Neurol. 2013 Oct;20(10):1390-7. doi: 10.1111/ene.12193. Epub 2013 May 22. PMID:23700969 doi:http://dx.doi.org/10.1111/ene.12193
  8. ↑ Huo Y, Khatri N, Hou Q, Gilbert J, Wang G, Man HY. The deubiquitinating enzyme USP46 regulates AMPA receptor ubiquitination and trafficking. J Neurochem. 2015 Sep;134(6):1067-80. doi: 10.1111/jnc.13194. Epub 2015 Jul 16. PMID:26077708 doi:http://dx.doi.org/10.1111/jnc.13194
  9. ↑ Vesa J, Hellsten E, Verkruyse LA, Camp LA, Rapola J, Santavuori P, Hofmann SL, Peltonen L. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis. Nature. 1995 Aug 17;376(6541):584-7. PMID:7637805 doi:http://dx.doi.org/10.1038/376584a0
  10. ↑ van Diggelen OP, Thobois S, Tilikete C, Zabot MT, Keulemans JL, van Bunderen PA, Taschner PE, Losekoot M, Voznyi YV. Adult neuronal ceroid lipofuscinosis with palmitoyl-protein thioesterase deficiency: first adult-onset patients of a childhood disease. Ann Neurol. 2001 Aug;50(2):269-72. PMID:11506414
  11. ↑ Renatus M, Parrado SG, D'Arcy A, Eidhoff U, Gerhartz B, Hassiepen U, Pierrat B, Riedl R, Vinzenz D, Worpenberg S, Kroemer M. Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure. 2006 Aug;14(8):1293-302. PMID:16905103 doi:10.1016/j.str.2006.06.012

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