Thioesterase: Difference between revisions

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{{STRUCTURE_1u8u|  PDB=1u8u  | SIZE=400| SCENE= |right|CAPTION=E. Coli Acyl-CoA thioesterase complex with octanoic acid, glycerol and sulfate [[1u8u]] }}
<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__
== Function ==
'''Thioesterase''' (TE) catalyzes the break of an ester bond to produce acid and alcohol at a thiol group. TEs are substrate-specific.<br />
*  '''Palmitoyl protein TE''' removes fatty acids like palmitate from modified cysteine residues during lysosomal degradation<ref>PMID:10737604</ref>.  For details see [[Palmitoyl protein thioesterase]].<br />
*  '''4-hydroxybenzoyl-CoA TE''' converts 4-hydroxybenzoyl-CoA to 4-hydroxybenzoate and CoA<ref>PMID:12732540</ref>.<br />
*  '''Acyl-CoA TE''' hydrolyzes acyl-CoA to the fatty acid and CoA and is involved in lipid metabolism<ref>PMID:11755680</ref>.  See also [[YbgC]] and [[Mitochondrial hotdog-fold thioesterase]].<br />
*  '''Fluoroacetyl-CoA TE''' from ''Streptomyces cattleya'' hydrolyzes fluoroacetyl-CoA thus preventing it from being metabolized to the lethal 4-hydroxy-trans-aconitate<ref>PMID:20836570</ref>.<br />
*  '''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<ref>PMID:24190967</ref>.  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.<br />
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* '''USP-L3''' hydrolyzes C-terminal adducts of UB and NEDD8.<br />
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* '''USP5''' cleaves multiubiquitin polymers.<br />
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* '''USP6''' has ATP-independent isopeptidase activity.<br />
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* '''USP7, USP4, USP13, USP15''' deubiquitinate several proteins.<br />
'''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.  '''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.  '''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 (UB).  The USPs are involved in the processing of poly-UB precursors and of ubiquinated proteins.  USP contains catalytic domain surrounded several domains:  Ub-like (UBL); Ub-associated (UBA); zinc finger-Ub-specific protease domain (UBP or DUSP); TRF homology domain.
* '''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.<br />
 
* '''USP11, USP14''' are proteasome-associated.<br />
* USP-L1, USP25 hydrolyze C-terminal adducts of UB.<br />
* '''USP12''' stabilizes T-cell complexes<ref>PMID:26811477</ref>.<br />
* USP-L3 hydrolyze C-terminal adducts of UB and NEDD8.<br />
* '''USP16, USP21''' deubiquitinate histone H2A.<br />
* USP5 cleaves multiubiquitin polymers.<br />
* '''USP18''' is a down regulator of the type I interferon signaling pathway<ref>PMID:23700969</ref>.<br />
* USP6 has ATP-independent isopeptidase activity.<br />
* '''USP28''' deubiquitinates proteins of the DNA damage pathway.<br />
* USP7, USP4, USP13, USP15 deubiquitinate several proteins.<br />
* '''USP33''' regulates centrosome duplication.<br />
* 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.<br />
* '''USP37''' deubiquitinates cyclin A.<br />
* USP11, USP14 are proteasome-associated.<br />
* '''USP46''' deubiquitinates AMPA receptor<ref>PMID:26077708</ref>.<br />
* USP16, USP21 deubiquitinate histone H2A.<br />
* USP28 deubiquitinates proteins of the DNA damage pathway.<br />
* USP33 regulates centrosome duplication.<br />
* USP37 deubiquitinates cyclin A.<br />


== Disease ==
Mutations in palmiotoyl protein TE cause neuronal ceroid lipocfuscinosis<ref>PMID:7637805</ref><ref>PMID:11506414</ref>.


== Structural highlights ==
<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>.
==3D structures of thioesterase==
==3D structures of thioesterase==
[[Thioesterase 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
 
'''Maristoyl-ACP-specific TE'''
 
[[1tht]] – TE – Vibrio harveyi
 
'''4-hydroxybenzoyl-CoA TE'''
 
[[1bvq]] – PsTE – ''Pseudomonas''<br />
[[1lo7]] – PsTE + 4-hydroxyphenyl CoA<br />
[[1lo9]] - PsTE (mutant) + 4-hydroxybenzoyl CoA<br />
[[1lo8]] - PsTE + 4-hydroxybenzyl CoA<br />
[[1q4s]] - ArTE + 4-hydroxybenzoate – '''Arthrobacte''r'<br />
[[1q4t]] - ArTE + 4-hydroxyphenyl CoA<br />
[[1q4u]] - ArTE + 4-hydroxybenzyl CoA<br />
[[3r32]], [[3r35]], [[3r37]], [[3r38]], [[3r3b]], [[3r3c]], [[3r3d]], [[3r3f]], [[3tea]] - ArTE (mutant) + 4-hydroxyphenacyl CoA<br />
[[3r36]] - ArTE (mutant) + 4-hydroxybenzoate<br />
[[3r3a]] - ArTE (mutant) + 4-hydroxybenzoate + CoA<br />
[[3r34]] - ArTE (mutant) + CoA<br />
 
'''Palmitoyl protein TE'''
 
[[1eh5]] – bTE1 + Palmitate – bovine<br />
[[1ei9]] – bTE1<br />
[[1exw]] – bTE1 + hexadecylsulfonyl fluoride<br />
[[1pja]] – hTEII – human<br />
[[3gro]] - hTEI
 
'''Acyl-CoA TE'''
 
[[1c8u]] – EcTEII – ''Escherichia coli''<br />
[[1ivn]] – EcTEI<br />
[[1jrl]] – EcTEI (mutant) <br />
[[1j00]] – EcTEI + diethyl phosphono derivative<br />
[[1v2g]], [[1u8u]] - EcTEI + octanoic acid<br />
[[2v1o]] – mTE7 hotdog domain – mouse<br />
[[2q2b]] – mTE7 C terminal<br />
[[3hlk]] – hTE2<br />
[[3k2i]] – hTE4<br />
[[2qq2]] - hTE7 C terminal<br />
[[3fo5]] – hTE11 START domain<br />
[[3b7k]] – hTE12<br />
[[3rd7]] – TE – ''Mycobacterium avium''<br />
[[3u0a]] – TEII – ''Mycobacterium marinum''<br />
[[1tbu]] – TE N terminal (peroximal) – yeast
 
'''Acyl protein TE'''
 
[[1fj2]] – EcTEI
 
'''Acyl-ACP TE'''
 
[[2ess]] – TE – ''Bacterioides thetaiotaomicron''<br />
[[4gak]] – TE – ''Spirosoma linguale''<br />
[[4gwh]] – TE – ''Yersinia pestis''<br />
 
'''ACP-polyene TE'''
 
[[4i4j]] – TE – ''Streptomyces globisporus''<br />
 
'''Fluoroacetyl-CoA TE'''
 
[[3kuv]], [[3kuw]], [[3kvi]] – ScTE (mutant) + acetate derivative – ''Streptomyces cattleya''<br />
[[3kv7]], [[3kv8]], [[3p2r]], [[3p2s]] – ScTE + acetate derivative<br />
[[3kvu]] – ScTE + acetyl-CoA<br />
[[3kvz]], [[3kw1]] – ScTE + FAcOPan<br />
[[3kx7]], [[3kx8]], [[3p2q]] – ScTE <br />
[[3p3f]] – ScTE (mutant) <br />
[[3p3i]] - ScTE (mutant) + acetate derivative + CoA<br />
 
'''DHNA-CoA TE'''
 
[[4k00]] – TE – ''Synechocystis''<br />
[[4k02]] – TE – ''Arabidopsis thaliana''<br />
 
'''Ubiquitin TE'''
 
''USP 2''
 
[[2zfy]] – hUSP – human  <BR />
[[2hd5]], [[3nhe]], [[3v6c]], [[3v6e]] – hUSP + Ub  <BR />
[[1tff]] – hUSP (mutant)  <BR />
[[2ibi]] – hUSP (mutant) + Ub <BR />
 
''USP 3''
 
[[2qiy]] – yUSP + USP-associated protein – yeast  <BR />
 
''USP 4''
 
[[2y6e]] – hUSP catalytic domain <br />
[[3jyu]] – mUSP N terminal domain - mouse<br />
 
''USP 5''
 
[[2dag]] – hUSP UBA domain 1 - NMR<br />
[[2dak]] – hUSP UBA domain 2 - NMR<br />
[[2g43]] – hUSP zinc finger USP domain<br />
[[2g45]] – hUSP zinc finger USP domain + Ub<br />
[[3ihp]] – hUSP + Ub  <BR />
 
''USP 7''
 
[[2f1z]] – hUSP<br />
[[1nb8]], [[4m5w]], [[4m5x]] – hUSP catalytic domain <br />
[[2kvr]] – hUSP UBL domain - NMR<br />
[[4pyz]] – hUSP UBL domains 1+2<br />
[[1yze]], [[2f1w]] – hUSP N terminal domain <br />
[[2ylm]] – hUSP C terminal domain <br />
[[2f1x]], [[2f1y]], [[2foj]], [[2foo]], [[2fop]] – hUSP N terminal domain/peptide <br />
 
''USP 7 complexes''
 
[[1nbf]] – hUSP catalytic domain + Ub aldehyde<br />
[[1yy6]] – hUSP N terminal domain + EBNA1 peptide<br />
[[2xxn]] – hUSP TRAF domain + VIRF-4 peptide<br />
[[3mqr]] – hUSP TRAF domain + HDMX peptide<br />
[[3mqs]] – hUSP TRAF domain + HDM2 peptide<br />
[[4jjq]] – hUSP TRAF domain + E2 peptide<br />
[[4kg9]] – hUSP TRAF domain + MCM-BP peptide<br />
 
''USP 8''
 
[[1whb]] – hUSP rhodanase domain – human - NMR<br />
[[2a9u]] – hUSP N terminal domain <br />
[[2gfo]] – hUSP catalytic domain <br />
 
''USP 8 complexes''
 
[[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 />
[[3n3k]] – hUSP catalytic domain + Ub<br />
 
''USP 11''
 
[[4mel]] – hUSP DUSP+UBL domains <br />
[[4mem]] – rUSP DUSP+UBL domains - rat<br />
 
''USP 13''
 
[[2l80]] – hUSP zinc finger domain - NMR<br />
[[2lbc]] – hUSP UBA domain - NMR<br />
 
''USP 14''
 
[[1wgg]] – mUSP N terminal domain - NMR<br />
[[2ayn]] – hUSP<br />
[[2ayo]] – hUSP + Ub aldehyde<br />
 
''USP 15''
 
[[3lmn]] – hUSP DUSP domain  <BR />
[[3ppa]], [[3pv1]], [[3t9l]], [[4a3o]], [[4a3p]] – hUSP DUSP+UBL domains <br />
[[1w6v]] – hUSP DUSP domain - NMR<br />
 
''USP 16''
 
[[2i50]] – hUSP zinc finger domain - NMR  <BR />
 
''USP 21''
 
[[3i3t]], [[2y5b]] – hUSP + Ub  <BR />
[[3mtn]] – hUSP + Ub inhibitor <BR />
 
''USP25''
 
[[1vdl]] – mUSP catalytic domain <br />
 
''USP 28''
 
[[2lva]] – hUSP N terminal - NMR  <BR />
 
''USP 33''
 
[[2uzg]] – hUSP zinc finger domain - NMR  <BR />
 
''USP 37''
 
[[3ihr]] – hUSP (mutant)  <BR />
[[3a7s]] – hUSP catalytic domain (mutant)  <BR />
 
''USP Cyld''
 
[[2vhf]] – hUSP  USP domain <BR />
 
''USP 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 />
 
''USP L3''
 
[[1uch]] – hUSP-L3  <br />
[[1xd3]] – hUSP-L3 + UBC<br />
[[2we6]] – PfUSP-L3 – ''Plasmodium falciparum''<br />
[[2wdt]] – PfUSP-L3 + Ub <br />
 
''USP L5''
 
[[3ris]] – hUSP catalytic domain  <BR />
[[3rii]], [[3a7s]] – hUSP catalytic domain (mutant)  <BR />
[[3tb3]] – hUSP UCH domain (mutant)  <BR />
[[3ihr]] – hUSP-L5 (mutant)  <br />
 
''USP ZranB1''
 
[[3zrh]] – hUSP  <BR />
 
''USP OTUB1''
 
[[3von]] – hUSP + E2 <BR />
[[4ddg]], [[4ddi]] – hUSP + Ub<BR />
[[4ddi]], [[4i6l]] – hUSP (mutant) + Ub<BR />
[[4dhz]] – 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 />
 
[[3znh]] – USP + Ub – Crimean-Congo hemorrhagic fever virus<BR />
 
'''RedJ TE'''
 
[[3qmv]], [[3qmw]] – TE –'' Streptomyces coelicolor''
 
'''Orf6 TE'''
 
[[4i45]] – TE – ''Photobacterium profundum''<br />
 
[[2av9]], [[2o5u]], [[2o6b]], [[2o6t]], [[2o6u]], [[3qy3]] – TE – ''Pseudomonas aeruginosa''


== References ==
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Latest revision as of 12:09, 5 January 2025

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[1]. For details see Palmitoyl protein thioesterase.
  • 4-hydroxybenzoyl-CoA TE converts 4-hydroxybenzoyl-CoA to 4-hydroxybenzoate and CoA[2].
  • Acyl-CoA TE hydrolyzes acyl-CoA to the fatty acid and CoA and is involved in lipid metabolism[3]. See also YbgC and Mitochondrial hotdog-fold thioesterase.
  • Fluoroacetyl-CoA TE from Streptomyces cattleya hydrolyzes fluoroacetyl-CoA thus preventing it from being metabolized to the lethal 4-hydroxy-trans-aconitate[4].
  • 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[5]. 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[6].
  • USP16, USP21 deubiquitinate histone H2A.
  • USP18 is a down regulator of the type I interferon signaling pathway[7].
  • USP28 deubiquitinates proteins of the DNA damage pathway.
  • USP33 regulates centrosome duplication.
  • USP37 deubiquitinates cyclin A.
  • USP46 deubiquitinates AMPA receptor[8].

Disease

Mutations in palmiotoyl protein TE cause neuronal ceroid lipocfuscinosis[9][10].

Structural highlights

. Ubiquitin thioesterase 2 active site contains the . The metal-binding enzyme contains a . The [11].

3D structures of thioesterase

Thioesterase 3D structures


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

ReferencesReferences

  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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