Thioesterase: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
Joel L. Sussman (talk | contribs)
ConfirmAccount, Editor, Journal, Mutation, Print3D, Tester, Bureaucrats, Administrators
7,980 edits
No edit summary
Michal Harel (talk | contribs)
31,761 edits
No edit summary
Line 66: Line 66:
**[[2pzh]] - TE - ''Helicobacter pylori''<br />
**[[2pzh]] - TE - ''Helicobacter pylori''<br />
**[[3rd7]] – TE – ''Mycobacterium avium''<br />
**[[3rd7]] – TE – ''Mycobacterium avium''<br />
**[[5t02]] – TE (mutant) + CoA + GDP – ''Neisseria meningitis''<br />
**[[5v3a]] – NmTE + CoA + GDP – ''Neisseria meningitis''<br />
**[[5t02]] – NmTE (mutant)  + CoA + GDP <br />
**[[5hz4]], [[5hwf]], [[5egk]] – SaTE (mutant)  – ''Staphylococcus aureus''<br />
**[[5hz4]], [[5hwf]], [[5egk]] – SaTE (mutant)  – ''Staphylococcus aureus''<br />
**[[4egj]] – SaTE + CoA<br />
**[[4egj]] – SaTE + CoA<br />
Line 91: Line 92:


**[[1fj2]] – EcTEI<br />
**[[1fj2]] – EcTEI<br />
**[[6avy]] – TE 2 - maize<br />
**[[5sym]] – hTE 1 + inhibitor<br />
**[[5sym]] – hTE 1 + inhibitor<br />
**[[5syn]] – hTE 2 + inhibitor<br />
**[[5syn]] – hTE 2 + inhibitor<br />
Line 128: Line 130:
*thioesterase
*thioesterase


**[[2av9]], [[2o5u]], [[2o6b]], [[2o6t]], [[2o6u]], [[3qy3]] – TE – ''Pseudomonas aeruginosa''
**[[2av9]], [[2o5u]], [[2o6b]], [[2o6t]], [[2o6u]], [[3qy3]], [[4qd7]] – PaTE – ''Pseudomonas aeruginosa''<br />
**[[4qda]], [[4qdb]] – PaTE (mutant)<br />
**[[4qd8]] – PaTE + phenacyl-CoA<br />
**[[4qd9]] – PaTE + benzoyl-CoA<br />


*Ubiquitin thioesterase
*Ubiquitin thioesterase or ubiquitin carboxyl-terminal hydrolase


*Ubiquitin thioesterase 2
*Ubiquitin thioesterase 2
Line 146: Line 151:


**[[2y6e]] – hUSP catalytic domain <br />
**[[2y6e]] – hUSP catalytic domain <br />
**[[5ctr]] – hUSP DUSP-UBL domain + SART3<br />
**[[3jyu]] – mUSP N terminal domain <br />
**[[3jyu]] – mUSP N terminal domain <br />


Line 152: Line 158:
**[[2dag]] – hUSP UBA domain 1 - NMR<br />
**[[2dag]] – hUSP UBA domain 1 - NMR<br />
**[[2dak]] – hUSP UBA domain 2 - NMR<br />
**[[2dak]] – hUSP UBA domain 2 - NMR<br />
**[[2g43]] – hUSP zinc finger USP domain<br />
**[[2g43]], [[6dxh]], [[6dxt]] – hUSP zinc finger USP domain<br />
**[[2g45]] – hUSP zinc finger USP domain + Ub<br />
**[[2g45]] – hUSP zinc finger USP domain + Ub<br />
**[[3ihp]] – hUSP + Ub  <BR />
**[[3ihp]] – hUSP + Ub  <BR />


*Ubiquitin thioesterase 7
*Ubiquitin thioesterase 7; domains - TRAF 63-205; catalytic 207-560; UBL1 537-664; UBL2 665-865


**[[2f1z]], [[5j7t]] – hUSP<br />
**[[2f1z]], [[5j7t]] – hUSP<br />
**[[1nb8]], [[4m5w]], [[4m5x]] – hUSP catalytic domain <br />
**[[1nb8]], [[4m5w]], [[4m5x]] – hUSP catalytic domain <br />
**[[5kyb]] – hUSP catalytic domain (mutant) <br />
**[[2kvr]] – hUSP UBL domain - NMR<br />
**[[2kvr]] – hUSP UBL domain - NMR<br />
**[[4pyz]], [[4wph]], [[4wpi]] – hUSP UBL domains 1+2<br />
**[[4pyz]], [[4wph]], [[4wpi]] – hUSP UBL domains 1+2<br />
**[[5fwi]] – hUSP catalytic + UBL domains 1+2<br />
**[[5fwi]], [[5j7t]] – hUSP catalytic + UBL domains 1+2<br />
**[[1yze]], [[2f1w]] – hUSP N terminal domain <br />
**[[1yze]], [[2f1w]] – hUSP TRAF domain <br />
**[[2ylm]] – hUSP C terminal domain <br />
**[[2ylm]] – hUSP C terminal domain <br />
**[[2f1x]], [[2f1y]], [[2foj]], [[2foo]], [[2fop]] – hUSP N terminal domain/peptide <br />
**[[2f1x]], [[2f1y]], [[2foj]], [[2foo]], [[2fop]] – hUSP TRAF domain/peptide <br />
**[[4zv3]] – mUSP N terminal domain <br />
**[[4zv3]] – mUSP N terminal domain <br />


Line 171: Line 178:


**[[1nbf]] – hUSP catalytic domain + Ub aldehyde<br />
**[[1nbf]] – hUSP catalytic domain + Ub aldehyde<br />
**[[5jtj]] – hUSP catalytic domain + Ub <br />
**[[5jtj]] – hUSP catalytic domain + polyubiquitin <br />
**[[1yy6]] – hUSP N terminal domain + EBNA1 peptide<br />
**[[5whc]], [[5n9r]], [[5n9t]], [[5uqv]], [[5uqx]], [[6f5h]] – hUSP catalytic domain + inhibitor<br />
**[[5kyc]], [[5kyd]], [[5kye]], [[5kyf]] – hUSP catalytic domain (mutant) + polyubiquitin <br />
**[[1yy6]] – hUSP TRAF domain + EBNA1 peptide<br />
**[[2xxn]] – hUSP TRAF domain + VIRF-4 peptide<br />
**[[2xxn]] – hUSP TRAF domain + VIRF-4 peptide<br />
**[[3mqr]] – hUSP TRAF domain + HDMX peptide<br />
**[[3mqr]] – hUSP TRAF domain + HDMX peptide<br />
**[[3mqs]] – hUSP TRAF domain + HDM2 peptide<br />
**[[3mqs]] – hUSP TRAF domain + HDM2 peptide<br />
**[[2fop]] – hUSP TRAF domain + MDM2 peptide<br />
**[[4jjq]] – hUSP TRAF domain + E2 peptide<br />
**[[4jjq]] – hUSP TRAF domain + E2 peptide<br />
**[[4kg9]] – hUSP TRAF domain + MCM-BP peptide<br />
**[[4kg9]] – hUSP TRAF domain + MCM-BP peptide<br />
**[[4ysi]] – hUSP TRAF domain + peptide<br />
**[[4ysi]], [[2foj]], [[2foo]] – hUSP TRAF domain + peptide<br />
**[[4yoc]] – hUSP residues 560-1102 + DNA methyl transferase<br />
**[[4yoc]], [[4z96]], [[4z97]] – hUSP residues 560-1102 + DNMT1<br />
**[[5c6d]] – hUSP residues 561-881 + UHRF1<br />
**[[5c6d]] – hUSP residues 561-881 + UHRF1<br />
**[[5c56]] – hUSP residues 560-1102 + Ub E3 ligase Icp0444w<br />
**[[5c56]] – hUSP residues 560-1102 + Ub E3 ligase Icp0444w<br />
Line 186: Line 196:


**[[1whb]] – hUSP rhodanase domain - NMR<br />
**[[1whb]] – hUSP rhodanase domain - NMR<br />
**[[2gwf]] – hUSP rhodanase domain + NRDP1br />
**[[2a9u]] – hUSP N terminal domain <br />
**[[2a9u]] – hUSP N terminal domain <br />
**[[2gfo]] – hUSP catalytic domain <br />
**[[2gfo]] – hUSP catalytic domain <br />
**[[3n3k]] – hUSP catalytic domain + ubiqitin<br />


*Ubiquitin thioesterase 8 complexes
*Ubiquitin thioesterase 8 complexes
Line 210: Line 222:
**[[5k16]] – hUSP <br />
**[[5k16]] – hUSP <br />
**[[5k1a]], [[5k1b]], [[5k1c]] – hUSP + WD repeat-containing protein<br />
**[[5k1a]], [[5k1b]], [[5k1c]] – hUSP + WD repeat-containing protein<br />
**[[5l8w]] – hUSP + WD repeat-containing protein + polyubiquitin<br />


*Ubiquitin thioesterase 13
*Ubiquitin thioesterase 13
Line 252: Line 265:


**[[2lva]], [[2muu]], [[2mux]] – hUSP N terminal - NMR  <BR />
**[[2lva]], [[2muu]], [[2mux]] – hUSP N terminal - NMR  <BR />
*Ubiquitin thioesterase 30
**[[5ohp]] – hUSP (mutant) + diubiquitin <BR />
**[[5ohk]], [[5ohn]] – hUSP (mutant) + polyubiquitin <BR />


*Ubiquitin thioesterase 33
*Ubiquitin thioesterase 33


**[[2uzg]] – hUSP zinc finger domain - NMR  <BR />
**[[2uzg]] – hUSP zinc finger domain - NMR  <BR />
*Ubiquitin thioesterase 35
**[[5txk]] – hUSP (mutant) + polyubiquitin <BR />


*Ubiquitin thioesterase 37
*Ubiquitin thioesterase 37
Line 284: Line 306:
**[[4dm9]] – hUSP + peptide inhibitor<BR />
**[[4dm9]] – hUSP + peptide inhibitor<BR />


*Ubiquitin thioesterase L3
*Ubiquitin thioesterase L3 or UCH-L3


**[[1uch]] – hUSP-L3  <br />
**[[1uch]] – hUSP-L3  <br />

Revision as of 21:23, 25 September 2018

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.
  • 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].

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

3D structures of thioesterase3D structures of thioesterase

Updated on 25-September-2018

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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Thioesterase&oldid=2949965"