Thioesterase

spinqualitylabelsall models Human ubiquitin esterase 2 (deepskyblue) complex with ubiquitin (green) and zinc+2 ion (grey) (PDB code 2hd5). Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function Thioesterase (TE) catalyzes the break of an ester bond to produce acid and alcohol at a thiol group. TEs are substrate-specific. Palmitoyl protein TE removes fatty acids like palmitate from modified cysteine residues during lysosomal degradation. For details see Palmitoyl protein thioesterase. 4-hydroxybenzoyl-CoA TE converts 4-hydroxybenzoyl-CoA to 4-hydroxybenzoate and CoA. Acyl-CoA TE hydrolyzes acyl-CoA to the fatty acid and CoA and is involved in lipid metabolism. See also YbgC. Fluoroacetyl-CoA TE from Streptomyces cattleya hydrolyzes fluoroacetyl-CoA thus preventing it from being metabolized to the lethal 4-hydroxy-trans-aconitate. Ubiquitin TE or ubiquitin carboxyl-terminal hydrolase (USP) removes conjugated ubiquitin (UB) from proteins thus regulating protein level by preventing their degradation. USP hydrolyze the peptide bond at the C-terminal glycine of ubiquitin. The USPs are involved in the processing of poly-UB precursors and of ubiquitinated proteins. USP contains catalytic domain surrounded several domains: Ub-like (UBL); Ub-associated (UBA); zinc finger-Ub-specific protease domain (UBP or DUSP); TRAF homology domain. USP-L1, USP25 hydrolyze C-terminal adducts of UB. USP-L3 hydrolyzes C-terminal adducts of UB and NEDD8. USP5 cleaves multiubiquitin polymers. USP6 has ATP-independent isopeptidase activity. USP7, USP4, USP13, USP15 deubiquitinate several proteins. USP8 removes conjugated ubiquitin from proteins thus preventing protein degradation. USP8 is involved in cell proliferation and is active in the M phase of proliferation. USP11, USP14 are proteasome-associated. USP12 stabilizes T-cell complexes. USP16, USP21 deubiquitinate histone H2A. USP18 is a down regulator of the type I interferon signaling pathway. USP28 deubiquitinates proteins of the DNA damage pathway. USP33 regulates centrosome duplication. USP37 deubiquitinates cyclin A. USP46 deubiquitinates AMPA receptor. Disease Mutations in palmiotoyl protein TE cause neuronal ceroid lipocfuscinosis. Structural highlights Human ubiquitin esterase 2 complex with ubiquitin and zinc+2 ion. Ubiquitin thioesterase 2 active site contains the catalytic triad Cys-His-Asn and the oxyanion hole Asn. 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.

3D structures of thioesterase

Updated on 22-September-2019

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• Maristoyl-ACP-specific thioesterase
  • Palmitoyl protein thioesterase – TE – Vibrio harveyi
• 4-hydroxybenzoyl-CoA thioesterase
  • YbgC – PsTE – Pseudomonas
    
  • 1lo7 – PsTE + 4-hydroxyphenyl CoA
    
  • 1lo9 - PsTE (mutant) + 4-hydroxybenzoyl CoA
    
  • 1lo8 - PsTE + 4-hydroxybenzyl CoA
    
  • 1q4s - ArTE + 4-hydroxybenzoate – 'Arthrobacter'
    
  • 1q4t - ArTE + 4-hydroxyphenyl CoA
    
  • 1q4u - ArTE + 4-hydroxybenzyl CoA
    
  • 3r32, 3r35, 3r37, 3r38, 3r3b, 3r3c, 3r3d, 3r3f, 3tea - ArTE (mutant) + 4-hydroxyphenacyl CoA
    
  • 3r36 - ArTE (mutant) + 4-hydroxybenzoate
    
  • 3r3a - ArTE (mutant) + 4-hydroxybenzoate + CoA
    
  • 3r34 - ArTE (mutant) + CoA
    
  • 6fdg – SaTE – Staphylococcus aureus
    
• Palmitoyl protein thioesterase
  • 1eh5 – bTE1 + Palmitate – bovine
    
  • 1ei9 – bTE1
    
  • 1exw – bTE1 + hexadecylsulfonyl fluoride
    
  • 1pja – hTEII – human
    
  • 3gro - hTEI
• Acyl-CoA thioesterase
  • 2pzh - TE - Helicobacter pylori
    
  • 3rd7 – TE – Mycobacterium avium
    
  • 5v3a – NmTE + CoA + GDP – Neisseria meningitis
    
  • 5t02 – NmTE (mutant) + CoA + GDP
    
  • 5hz4, 5hwf, 5egk – SaTE (mutant) – Staphylococcus aureus
    
  • 4egj – SaTE + CoA
    
  • 1ivn, 5tic – EcTEI – Escherichia coli
    
  • 1jrl – EcTEI (mutant)
    
  • 1j00 – EcTEI + diethyl phosphono derivative
    
  • 1v2g, 1u8u - EcTEI + octanoic acid
    
  • 5tid, 5tie, 5tif - EcTEI (mutant) + octanoic acid
    
  • 1tbu – TEI N terminal (peroximal) – yeast
    
  • 1c8u – EcTEII
    
  • 3u0a – TEII – Mycobacterium marinum
    
  • 4qfw – YpTE II – Yersinia pestis
    
  • 4r4u – YpTE II + CoA
    
  • 3hlk – hTE2
    
  • 3k2i – hTE4
    
  • 2qq2 - hTE7 C terminal
    
  • 2v1o – mTE7 hotdog domain – mouse
    
  • 2q2b – mTE7 C terminal
    
  • 3fo5 – hTE11 START domain
    
  • 3b7k, 4moc – hTE12
    
  • 4mob – hTE12 + ADP
    
• Acyl protein thioesterase
  • 1fj2 – EcTEI
    
  • 6avy – TE 2 - maize
    
  • 5sym – hTE 1 + inhibitor
    
  • 5syn – hTE 2 + inhibitor
    
• Acyl-ACP thioesterase
  • 2ess – TE – Bacterioides thetaiotaomicron
    
  • 4gak – TE – Spirosoma linguale
    
• ACP-polyene thioesterase
  • 4i4j – TE – Streptomyces globisporus
    
• Fluoroacetyl-CoA thioesterase
  • 3kuv, 3kuw, 3kvi – ScTE (mutant) + acetate derivative – Streptomyces cattleya
    
  • 3kv7, 3kv8, 3p2r, 3p2s – ScTE + acetate derivative
    
  • 3kvu – ScTE + acetyl-CoA
    
  • 3kvz, 3kw1 – ScTE + FAcOPan
    
  • 3kx7, 3kx8, 3p2q – ScTE
    
  • 3p3f – ScTE (mutant)
    
  • 3p3i - ScTE (mutant) + acetate derivative + CoA
    
• Dihydroxynaphthoyl-CoA thioesterase
  • 4k00 – TE – Synechocystis
    
  • 4k02 – AtTE – Arabidopsis thaliana
    
• RedJ thioesterase
  • 3qmv, 3qmw – TE – Streptomyces coelicolor
• Orf6 thioesterase
  • 4i45 – TE – Photobacterium profundum
    
• thioesterase
  • 2av9, 2o5u, 2o6b, 2o6t, 2o6u, 3qy3, 4qd7 – PaTE – Pseudomonas aeruginosa
    
  • 4qda, 4qdb – PaTE (mutant)
    
  • 4qd8 – PaTE + phenacyl-CoA
    
  • 4qd9 – PaTE + benzoyl-CoA
    
• Ubiquitin thioesterase or ubiquitin carboxyl-terminal hydrolase
• Ubiquitin thioesterase 2
  • 2zfy – hUSP – human
    
  • 2hd5, 3nhe, 3v6c, 3v6e – hUSP + Ub
    
  • 1tff – hUSP (mutant)
    
  • 2ibi – hUSP (mutant) + Ub
    
• Ubiquitin thioesterase 3
  • 2qiy – yUSP + USP-associated protein
    
• Ubiquitin thioesterase 4
  • 2y6e – hUSP catalytic domain
    
  • 5ctr – hUSP DUSP-UBL domain + SART3
    
  • 3jyu – mUSP N terminal domain
    
• Ubiquitin thioesterase 5
  • 2dag – hUSP UBA domain 1 - NMR
    
  • 2dak – hUSP UBA domain 2 - NMR
    
  • 2g43, 6dxh, 6dxt – hUSP zinc finger USP domain
    
  • 2g45 – hUSP zinc finger USP domain + Ub
    
  • 3ihp – hUSP + Ub
    
• Ubiquitin thioesterase 7; domains - TRAF 63-205; catalytic 207-560; UBL1 537-664; UBL2 665-865
  • 2f1z, 5j7t – hUSP
    
  • 1nb8, 4m5w, 4m5x – hUSP catalytic domain
    
  • 5kyb – hUSP catalytic domain (mutant)
    
  • 2kvr – hUSP UBL domain - NMR
    
  • 4pyz, 4wph, 4wpi – hUSP UBL domains 1+2
    
  • 5fwi, 5j7t – hUSP catalytic + UBL domains 1+2
    
  • 1yze, 2f1w – hUSP TRAF domain
    
  • 2ylm – hUSP C terminal domain
    
  • 2f1x, 2f1y, 2foj, 2foo, 2fop – hUSP TRAF domain/peptide
    
  • 4zv3 – mUSP N terminal domain
    
• Ubiquitin thioesterase 7 complexes
  • 1nbf – hUSP catalytic domain + Ub aldehyde
    
  • 5jtj – hUSP catalytic domain + polyubiquitin
    
  • 5whc, 5n9r, 5n9t, 5uqv, 5uqx, 6f5h – hUSP catalytic domain + inhibitor
    
  • 5kyc, 5kyd, 5kye, 5kyf – hUSP catalytic domain (mutant) + polyubiquitin
    
  • 1yy6 – hUSP TRAF domain + EBNA1 peptide
    
  • 2xxn – hUSP TRAF domain + VIRF-4 peptide
    
  • 3mqr – hUSP TRAF domain + HDMX peptide
    
  • 3mqs – hUSP TRAF domain + HDM2 peptide
    
  • 2fop – hUSP TRAF domain + MDM2 peptide
    
  • 4jjq – hUSP TRAF domain + E2 peptide
    
  • 4kg9 – hUSP TRAF domain + MCM-BP peptide
    
  • 4ysi, 2foj, 2foo – hUSP TRAF domain + peptide
    
  • 4yoc, 4z96, 4z97 – hUSP residues 560-1102 + DNMT1
    
  • 5c6d – hUSP residues 561-881 + UHRF1
    
  • 5c56 – hUSP residues 560-1102 + Ub E3 ligase Icp0444w
    
• Ubiquitin thioesterase 8
  • 1whb – hUSP rhodanase domain - NMR
    
  • 2gwf – hUSP rhodanase domain + NRDP1br />
  • 2a9u – hUSP N terminal domain
    
  • 2gfo – hUSP catalytic domain
    
  • 3n3k – hUSP catalytic domain + ubiqitin
    
• Ubiquitin thioesterase 8 complexes
  • 2gwf – hUSP rhodanase domain + ring finger protein 41 USP8 interaction domain
    
  • 3mhh, 3m99, 4fip, 4fjc, 4f5k, 4fk5 – yUSP + SUS1 + SGF11 +SGF73
    
  • 3mhs – yUSP + SUS1 + SGF11 +SGF73 + Ub
    
  • 4zux – yUSP + SUS1 + SGF11 +SGF73 + Ub + Histones H3,2, H4, H2A, H2B + DNA
    
  • 3n3k – hUSP catalytic domain + Ub
    
• Ubiquitin thioesterase 9
  • 5vbd – hUSP 9x UBL domain
    
• Ubiquitin thioesterase 11
  • 4mel – hUSP DUSP+UBL domains
    
  • 4mem – rUSP DUSP+UBL domains - rat
    
• Ubiquitin thioesterase 12
  • 5k16 – hUSP
    
  • 5k1a, 5k1b, 5k1c – hUSP + WD repeat-containing protein
    
  • 5l8w – hUSP + WD repeat-containing protein + polyubiquitin
    
• Ubiquitin thioesterase 13
  • 2l80 – hUSP zinc finger domain - NMR
    
  • 2lbc – hUSP UBA domain - NMR
    
• Ubiquitin thioesterase 14
  • 1wgg – mUSP N terminal domain - NMR
    
  • 2ayn – hUSP
    
  • 2ayo – hUSP + Ub aldehyde
    
  • 1wiv – AtUSP UBA domain - NMR
    
  • 5gjq – hUSP in proteasome – Cryo EM
    
• Ubiquitin thioesterase 15
  • 3lmn – hUSP DUSP domain
    
  • 3ppa, 3pv1, 3t9l, 4a3o, 4a3p – hUSP DUSP+UBL domains
    
  • 1w6v – hUSP DUSP domain - NMR
    
  • 5jjw – hUSP catalytic domain + SART HAT domain
    
  • 5ctr – hUSP DUSP+UBL domains + SART HAT domain
    
• Ubiquitin thioesterase 16
  • 2i50 – hUSP zinc finger domain - NMR
    
• Ubiquitin thioesterase 18
  • 5cht – hUSP
    
• Ubiquitin thioesterase 21
  • 3i3t, 2y5b – hUSP + Ub
    
  • 3mtn – hUSP + Ub inhibitor
    
• Ubiquitin thioesterase 25
  • 1vdl – mUSP catalytic domain
    
• Ubiquitin thioesterase 28
  • 2lva, 2muu, 2mux – hUSP N terminal - NMR
    
• Ubiquitin thioesterase 30
  • 5ohp – hUSP (mutant) + diubiquitin
    
  • 5ohk, 5ohn – hUSP (mutant) + polyubiquitin
    
• Ubiquitin thioesterase 33
  • 2uzg – hUSP zinc finger domain - NMR
    
• Ubiquitin thioesterase 35
  • 5txk – hUSP (mutant) + polyubiquitin
    
• Ubiquitin thioesterase 37
  • 3ihr – hUSP (mutant)
    
  • 3a7s – hUSP catalytic domain (mutant)
    
  • 3u12 – hUSP pleckstrin domain
    
• Ubiquitin thioesterase 38
  • 4rxx – hUSP N terminal
    
• Ubiquitin thioesterase 46
  • 5cvm – hUSP + Ub
    
  • 5cvn, 5cvo – hUSP + WD repeat-containing protein + Ub
    
• Ubiquitin thioesterase Cyld
  • 2vhf – hUSP USP domain
    
• Ubiquitin thioesterase L1
  • 2etl – hUSP-L1
    
  • 3irt, 4jkj – hUSP (mutant)
    
  • 2len – hUSP (mutant) - NMR
    
  • 3ifw, 3kvf, 3kw5 – hUSP (mutant) + Ub
    
  • 4dm9 – hUSP + peptide inhibitor
    
• Ubiquitin thioesterase L3 or UCH-L3
  • 1uch – hUSP-L3
    
  • 1xd3 – hUSP-L3 + UBC
    
  • 2we6 – PfUSP-L3 – Plasmodium falciparum
    
  • 2wdt – PfUSP-L3 + Ub
    
• Ubiquitin thioesterase L5
  • 3ris – hUSP catalytic domain
    
  • 3rii, 3a7s – hUSP catalytic domain (mutant)
    
  • 3tb3 – hUSP UCH domain (mutant)
    
  • 3ihr – hUSP-L5 (mutant)
    
  • 4uel – hUSP-L5 + polyUb + proteasomal Ub receptor Deubad domain
    
  • 4uem – hUSP-L5 + proteasomal Ub receptor Deubad domain
    
  • 4wlq – mUSP-L5 + proteasomal Ub receptor C terminal
    
  • 4wlr – mUSP-L5 + polyUb + proteasomal Ub receptor C terminal
    
  • 4uf5, 4wlp – hUSP-L5 + nuclear factor Deubad domain
    
  • 4uf6 – hUSP-L5 + polyUb + nuclear factor Deubad domain
    
• Ubiquitin thioesterase ZranB1
  • 3zrh – hUSP
    
  • 4s1z – bUSP zinc finger + Ub
    
• Ubiquitin thioesterase OTUB1
  • 3von – hUSP + E2
    
  • 4ddg, 4ddi – hUSP + Ub
    
  • 4i6l – hUSP (mutant) + Ub
    
  • 4dhz, 4ldt – hUSP + E2 + Ub
    
  • 4boq - hUSP OTU domain
    
  • 4boz - hUSP OTU domain (mutant) + Ub
    
  • 4bos - hUSP OTU domain (mutant) + Ub + OTUD2 peptide
    
  • 4fjv - hUSP OTUB2 + Ub
    
  • 4dhj – nUSP + E2 + Ub - nematode
    
  • 4dhi – nUSP + E2
    
  • 2kzr – mUSP UBX-like domain – NMR
    
  • 4kdi, 4kdl – yUSP UBX-like domain + transitional endoplasmic reticulum ATPase
    
  • 3by4, 3c0r - yUSP OTU domain + Ub
    
• Ubiquitin thioesterase
  • 3znh – USP OTU domain + Ub – Crimean-Congo hemorrhagic fever virus
    
• Pseudomonas aeruginosa TE
  • 2av9, 2o5u, 2o6b, 2o6t, 2o6u, 3qy3 – PaTE – Pseudomonas aeruginosa
    
  • 4qd7 – PaTE hotdog domain
    
  • 4qda, 4qdb – PaTE hotdog domain (mutant)
    
  • 4qd8, 4dq9 – PaTE hotdog domain + acyl-CoA derivatives
    
• Thioesterase
  • 5vpj – TE – Actinomadura verrucosospora
    
  • 5dio, 5byu – TE – Legionella pneumophila
    

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Michal Harel, Alexander Berchansky, Joel L. Sussman