{"uniprot":"A8MYZ0","gene":"MINDY4B","name":"Inactive ubiquitin carboxyl-terminal hydrolase MINDY-4B","organism":"Homo sapiens (Human)","status":"dark","length":460,"sequence":"MDMEVLGQEQSSEQLDLEEISRKISFLDKWREIFSYHRLGTNNSTPQNHEGNHTSADENEDGTGLSQPKGQGHLPSSGLCSIPNPSIISSKLGGFPISLAMATKLRQILFGNTVHVFSYNWKKAYFRFHDPSSELAFTLEVGKGGARSIQMAVQGSIIKYLLFTRKGKDCNLGNLCEISKKEQEQALAAALAGILWAAGAAQKATICLVTEDIYVASTPDYSVDNFTERLQLFEFLEKEAAEKFIYDHLLCFRGEGSHGVILFLYSLIFSRTFERLQMDLDVTTTQLLQPNAGGFLCRQAVLNMILTGRASPNVFNGCEEGKSQETLHGVLTRSDVGYLQWGKDASEDDRLSQVGSMLKTPKLPIWLCNINGNYSILFCTNRQLLSDWKMERLFDLYFYSGQPSQKKLVRLTIDTHSHHWERDQQEEKHGPRRRFSPVEMAIRTKWSEATINWNGTVPFF","function_summary":"A soluble human deubiquitinase that resides in the cytosol and removes ubiquitin from modified proteins and polyubiquitin chains. Its catalytic cysteine protease core hydrolyzes isopeptide bonds within both degradation- and signaling-linked ubiquitin architectures, thereby dampening proteasome-directed turnover and attenuating endoplasmic reticulum–associated degradation throughput. By engaging ubiquitin-modified substrates and proteostasis assemblies through multivalent binding, it fine-tunes ubiquitin signaling and proteome quality control within the cytoplasm.","plain_language":"MINDY4B has barely been studied. The model's best guess: A soluble human deubiquitinase that resides in the cytosol and removes ubiquitin from modified proteins and polyubiquitin chains. Its catalytic cysteine protease core hydrolyzes isopeptide bonds within both degradation- and signaling-linked ubiquitin architectures, thereby dampening proteasome-directed turnover and attenuating endoplasmic reticulum–associated degradation throughput.","uniprot_summary":"Hydrolase that can remove conjugated ubiquitin from proteins and polyubiquitin chains. Can hydrolyze ATP- and GTP-dependent polyubiquitination.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"},{"id":"GO:0004843","label":"cysteine-type deubiquitinase activity"}],"biological_process":[{"id":"GO:1904293","label":"negative regulation of ERAD pathway"},{"id":"GO:1901799","label":"negative regulation of proteasomal protein catabolic process"},{"id":"GO:0070536","label":"protein K63-linked deubiquitination"},{"id":"GO:0071108","label":"protein K48-linked deubiquitination"}],"cellular_component":[{"id":"GO:0005829","label":"cytosol"}]},"interpro":[{"id":"IPR025257","name":"Deubiquitinating enzyme MINDY-3/4, conserved domain","type":"domain","start":106,"end":455},{"id":"IPR039785","name":"Deubiquitinating enzyme MINDY-3/4","type":"family","start":15,"end":459}],"reasoning":"I begin with the InterPro architecture. The polypeptide carries IPR039785 (Deubiquitinating enzyme MINDY-3/4 family) spanning residues 15–459, which frames the entire catalytic core and accessory regions characteristic of MINDY-type deubiquitinases. Nested within this, IPR025257 (Deubiquitinating enzyme MINDY-3/4, conserved domain) occupies residues 106–455, defining the central catalytic module. This ordered layout—an N-terminal family-defining envelope followed by a long conserved catalytic domain—establishes a cysteine protease fold that cleaves isopeptide bonds within polyubiquitin chains. The conserved MINDY core dictates cysteine-type deubiquitinase chemistry and explains the ability to hydrolyze both ATP- and GTP-dependent ubiquitin conjugation states by attacking the isopeptide linkage with a catalytic cysteine and general acid–base residues.\n\nFrom this architecture, the molecular function resolves into two complementary activities. First, the enzyme’s catalytic core enacts GO:0004843 cysteine-type deubiquitinase activity, directly reversing ubiquitination. Second, the extended family scaffold and exposed surfaces typical of MINDY enzymes support multivalent contacts with substrates and cofactors, accounting for GO:0005515 protein binding. The combination of catalytic and binding capacities allows selective engagement of ubiquitin chains and their associated complexes.\n\nThe catalytic profile of MINDY-type enzymes explains the biological processes they drive. By trimming or removing ubiquitin chains, the enzyme executes GO:0071108 protein K48-linked deubiquitination and GO:0070536 protein K63-linked deubiquitination. While K48 chains target substrates to the proteasome and K63 chains scaffold signaling and ER-associated pathways, MINDY-mediated hydrolysis can attenuate both, thereby buffering ubiquitin flux. This deubiquitination causally leads to GO:1901799 negative regulation of proteasomal protein catabolic process by reducing substrate commitment to degradation. In the endoplasmic reticulum-associated degradation axis, selective removal of ubiquitin from ERAD substrates or pathway components dampens throughput, aligning with GO:1904293 negative regulation of ERAD pathway.\n\nCellular placement follows from function and sequence context. The absence of transmembrane segments and the soluble catalytic architecture point to a cytosolic enzyme that surveys ubiquitin-modified clients and proteostasis machinery. This supports localization to GO:0005829 cytosol and is consistent with a broader cytoplasmic residency where ERAD substrates and proteasome-bound complexes are triaged.\n\nMechanistically, the enzyme likely recognizes and binds polyubiquitin via surfaces in the MINDY conserved domain, positions the isopeptide bond for nucleophilic attack by its catalytic cysteine, and resolves the acyl-enzyme intermediate to release free ubiquitin. By acting on both K48 and K63 architectures, it modulates proteasome-directed degradation and ERAD throughput. I hypothesize transient assemblies with ubiquitin-chain readers and ERAD adaptors: cytosolic UBA/UBL shuttles and ER-proximal complexes that hand substrates to the proteasome. Such assemblies would allow the enzyme to fine-tune ubiquitin signaling in the cytosol and at ER–cytosol interfaces.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-A8MYZ0.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/A8MYZ0"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/A8MYZ0/entry","atlas":"/p/A8MYZ0"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}