JAMM1_PYRFU
ID JAMM1_PYRFU Reviewed; 140 AA.
AC Q8U1Y4;
DT 25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=Desampylase {ECO:0000305|PubMed:28479062};
DE EC=3.4.19.15 {ECO:0000269|PubMed:28479062};
DE AltName: Full=JAMM/MPN(+) metalloprotease {ECO:0000303|PubMed:28479062};
DE AltName: Full=PfJAMM1 {ECO:0000303|PubMed:28479062};
GN OrderedLocusNames=PF1070 {ECO:0000312|EMBL:AAL81194.1};
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [2] {ECO:0007744|PDB:5LD9, ECO:0007744|PDB:5LDA}
RP X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) IN COMPLEXES WITH ZINC AND THE
RP UBIQUITIN-LIKE PROTEIN SAMP2, DISULFIDE BONDS, FUNCTION, CATALYTIC
RP ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION,
RP SUBUNIT, AND MUTAGENESIS OF GLU-34; 69-MET--GLU-74; LEU-70; CYS-93; ASP-101
RP AND TRP-108.
RX PubMed=28479062; DOI=10.1016/j.str.2017.04.002;
RA Cao S., Engilberge S., Girard E., Gabel F., Franzetti B.,
RA Maupin-Furlow J.A.;
RT "Structural insight into ubiquitin-like protein recognition and oligomeric
RT states of JAMM/MPN+ proteases.";
RL Structure 25:823-833(2017).
CC -!- FUNCTION: Metalloprotease that displays desampylase (DSAMP) activity,
CC cleaving ubiquitin-like small archaeal modifier proteins (SAMP1, SAMP2
CC and SAMP3) from protein conjugates (isopeptide- and linear-linked).
CC Thus, likely regulates sampylation and the pools of 'free' SAMP
CC available for protein modification. In vitro, is also able to cleave
CC non-physiological ubiquitin (Ub) substrates, such as 'Met1-', 'Lys48-',
CC and 'Lys63'-linked Ub dimers (Ub2), and to remove Ub tags from diverse
CC proteins. {ECO:0000269|PubMed:28479062}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N(6)-[small archaeal modifier protein]-[protein]-L-lysine +
CC H2O = a [protein]-L-lysine + a [small archaeal modifier protein].;
CC EC=3.4.19.15; Evidence={ECO:0000269|PubMed:28479062};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:28479062};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:28479062};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA in vitro.
CC {ECO:0000269|PubMed:28479062}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=14.2 uM for SAMP2 dimer (with PfJAMM1 in the dimeric form, at 100
CC degrees Celsius) {ECO:0000269|PubMed:28479062};
CC KM=15.5 uM for SAMP2 dimer (with PfJAMM1 in the monomeric form, at
CC 100 degrees Celsius) {ECO:0000269|PubMed:28479062};
CC KM=155 uM for M1-linked Ub dimer (with PfJAMM1 in the monomeric form,
CC at 70 degrees Celsius) {ECO:0000269|PubMed:28479062};
CC Note=kcat is 0.28 min(-1) for the cleavage of SAMP2 dimer using
CC PfJAMM1 in the dimeric form. kcat is 0.16 min(-1) for the cleavage of
CC SAMP2 dimer using PfJAMM1 in the monomeric form (at 100 degrees
CC Celsius). kcat is 0.0016 min(-1) for the cleavage of M1-linked Ub
CC dimer using PfJAMM1 in the monomeric form (at 70 degrees Celsius).
CC {ECO:0000269|PubMed:28479062};
CC Temperature dependence:
CC Optimum temperature is 100 degrees Celsius.
CC {ECO:0000269|PubMed:28479062};
CC -!- SUBUNIT: Exists in two major states: monomer and homodimer. Both
CC conformational states are catalytically active.
CC {ECO:0000269|PubMed:28479062}.
CC -!- PTM: The disulfide bridge probably stabilizes the PfJAMM1 homodimer at
CC the optimal growth temperature of the hyperthermophile.
CC {ECO:0000305|PubMed:28479062}.
CC -!- SIMILARITY: Belongs to the peptidase M67B family. {ECO:0000305}.
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DR EMBL; AE009950; AAL81194.1; -; Genomic_DNA.
DR RefSeq; WP_011012207.1; NZ_CP023154.1.
DR PDB; 5LD9; X-ray; 1.73 A; A/B=1-140.
DR PDB; 5LDA; X-ray; 1.90 A; A=11-140.
DR PDBsum; 5LD9; -.
DR PDBsum; 5LDA; -.
DR AlphaFoldDB; Q8U1Y4; -.
DR SMR; Q8U1Y4; -.
DR STRING; 186497.PF1070; -.
DR EnsemblBacteria; AAL81194; AAL81194; PF1070.
DR GeneID; 41712879; -.
DR KEGG; pfu:PF1070; -.
DR PATRIC; fig|186497.12.peg.1130; -.
DR eggNOG; arCOG01138; Archaea.
DR HOGENOM; CLU_116765_4_2_2; -.
DR OMA; GIFHSHL; -.
DR OrthoDB; 101895at2157; -.
DR PhylomeDB; Q8U1Y4; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0070122; F:isopeptidase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140492; F:metal-dependent deubiquitinase activity; IEA:InterPro.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR InterPro; IPR028090; JAB_dom_prok.
DR InterPro; IPR000555; JAMM/MPN+_dom.
DR InterPro; IPR037518; MPN.
DR Pfam; PF14464; Prok-JAB; 1.
DR SMART; SM00232; JAB_MPN; 1.
DR PROSITE; PS50249; MPN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Hydrolase; Metal-binding; Metalloprotease;
KW Protease; Reference proteome; Zinc.
FT CHAIN 1..140
FT /note="Desampylase"
FT /id="PRO_0000441760"
FT DOMAIN 13..133
FT /note="MPN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT MOTIF 88..101
FT /note="JAMM motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT ACT_SITE 34
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:D4GTS4"
FT BINDING 88
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:28479062,
FT ECO:0007744|PDB:5LD9"
FT BINDING 90
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:28479062,
FT ECO:0007744|PDB:5LD9"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:28479062,
FT ECO:0007744|PDB:5LD9"
FT SITE 98
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:D4GTS4"
FT DISULFID 93
FT /note="Interchain"
FT /evidence="ECO:0000269|PubMed:28479062,
FT ECO:0007744|PDB:5LD9"
FT MUTAGEN 34
FT /note="E->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:28479062"
FT MUTAGEN 69..74
FT /note="MLKALE->AAKAAA: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:28479062"
FT MUTAGEN 70
FT /note="L->A: 2.4-fold decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:28479062"
FT MUTAGEN 93
FT /note="C->S: Is still catalytically active."
FT /evidence="ECO:0000269|PubMed:28479062"
FT MUTAGEN 101
FT /note="D->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:28479062"
FT MUTAGEN 108
FT /note="W->A: Nearly no effect on substrate affinity."
FT /evidence="ECO:0000269|PubMed:28479062"
FT STRAND 13..16
FT /evidence="ECO:0007829|PDB:5LD9"
FT HELIX 18..30
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 45..52
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 62..64
FT /evidence="ECO:0007829|PDB:5LDA"
FT HELIX 66..78
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 82..93
FT /evidence="ECO:0007829|PDB:5LD9"
FT HELIX 99..107
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 110..116
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:5LD9"
FT STRAND 132..139
FT /evidence="ECO:0007829|PDB:5LD9"
SQ SEQUENCE 140 AA; 16018 MW; 8427B48D7218D4D3 CRC64;
MPSSSKSDFS FSTLIIPQHY LRAILKVVSS SSVEVCGFLF GKENRVLKVR FIRNRLNSPV
EFEMDPEEML KALEEAEQEN LEVVGIFHSH IACPPIPSGK DLEGMKRWPV IWLIVNEKGE
YKAWILSEKN KISEVKIVVE
