ARMT1_YEAST
ID ARMT1_YEAST Reviewed; 470 AA.
AC Q04371; D6VZK1;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Damage-control phosphatase YMR027W {ECO:0000303|PubMed:27322068};
DE EC=3.1.3.- {ECO:0000269|PubMed:27322068};
DE AltName: Full=Sugar phosphate phosphatase YMR027W {ECO:0000303|PubMed:27322068};
GN OrderedLocusNames=YMR027W; ORFNames=YM9711.17;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP INDUCTION.
RX PubMed=11598186; DOI=10.1091/mbc.12.10.2987;
RA Gasch A.P., Huang M., Metzner S., Botstein D., Elledge S.J., Brown P.O.;
RT "Genomic expression responses to DNA-damaging agents and the regulatory
RT role of the yeast ATR homolog Mec1p.";
RL Mol. Biol. Cell 12:2987-3003(2001).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP DISRUPTION PHENOTYPE.
RX PubMed=18085829; DOI=10.1371/journal.pgen.0030228;
RA Alvaro D., Lisby M., Rothstein R.;
RT "Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting
RT recombination.";
RL PLoS Genet. 3:E228-E228(2007).
RN [6] {ECO:0007744|PDB:3PT1, ECO:0007744|PDB:5BY0, ECO:0007744|PDB:5F13}
RP X-RAY CRYSTALLOGRAPHY (1.77 ANGSTROMS) IN COMPLEXES WITH MANGANESE AND
RP FRUCTOSE-6-PHOSPHATE, FUNCTION, DOMAIN, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, COFACTOR, MUTAGENESIS
RP OF GLU-110; TYR-114; ASN-192; ASP-254; ASN-255; GLU-259; ASP-263; SER-291;
RP ASP-292; LYS-382; ASP-384; ARG-420 AND LYS-423, AND DISRUPTION PHENOTYPE.
RX PubMed=27322068; DOI=10.1038/nchembio.2108;
RA Huang L., Khusnutdinova A., Nocek B., Brown G., Xu X., Cui H., Petit P.,
RA Flick R., Zallot R., Balmant K., Ziemak M.J., Shanklin J.,
RA de Crecy-Lagard V., Fiehn O., Gregory J.F. III, Joachimiak A.,
RA Savchenko A., Yakunin A.F., Hanson A.D.;
RT "A family of metal-dependent phosphatases implicated in metabolite damage-
RT control.";
RL Nat. Chem. Biol. 12:621-627(2016).
CC -!- FUNCTION: Metal-dependent phosphatase that shows phosphatase activity
CC against several substrates, including fructose-1-phosphate and
CC fructose-6-phosphate (PubMed:27322068). Its preference for fructose-1-
CC phosphate, a strong glycating agent that causes DNA damage rather than
CC a canonical yeast metabolite, suggests a damage-control function in
CC hexose phosphate metabolism (PubMed:27322068).
CC {ECO:0000269|PubMed:27322068}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-fructose 1-phosphate + H2O = D-fructose + phosphate;
CC Xref=Rhea:RHEA:35603, ChEBI:CHEBI:15377, ChEBI:CHEBI:37721,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:138881;
CC Evidence={ECO:0000269|PubMed:27322068};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-fructose 6-phosphate = D-glyceraldehyde 3-phosphate +
CC dihydroxyacetone; Xref=Rhea:RHEA:28002, ChEBI:CHEBI:16016,
CC ChEBI:CHEBI:57634, ChEBI:CHEBI:59776;
CC Evidence={ECO:0000269|PubMed:27322068};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:27322068};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:27322068};
CC Note=Phosphatase activity is strongly promoted by several divalent
CC cations but is it suggested that Mn(2+) and possibly Ni(2+) represent
CC biologically relevant metal ion cofactors for damage-control
CC phosphatases. {ECO:0000269|PubMed:27322068};
CC -!- ACTIVITY REGULATION: Activity is strongly promoted by Co(2+), Ni(2+)
CC and Mn(2+) (PubMed:27322068). Activity is inhibited by EDTA
CC (PubMed:27322068). {ECO:0000269|PubMed:27322068}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=310 uM for fructose-1-phosphate {ECO:0000269|PubMed:27322068};
CC KM=300 uM for fructose-6-phosphate {ECO:0000269|PubMed:27322068};
CC KM=490 uM for mannose-6-phosphate {ECO:0000269|PubMed:27322068};
CC KM=280 uM for 2-desoxyribose-5-phosphate
CC {ECO:0000269|PubMed:27322068};
CC KM=7.5 uM for Co(2+) {ECO:0000269|PubMed:27322068};
CC KM=8.8 uM for Zn(2+) {ECO:0000269|PubMed:27322068};
CC Note=kcat is 11.6 sec(-1) with fructose-1-phosphate as substrate.
CC kcat is 4.2 sec(-1) with fructose-6-phosphate as substrate. kcat is
CC 3.3 sec(-1) with mannose-6-phosphate as substrate. kcat is 1.9 sec(-
CC 1) with 2-desoxyribose-5-phosphate as substrate.
CC {ECO:0000269|PubMed:27322068};
CC -!- INDUCTION: Expression is up-regulated in response to treatment with the
CC DNA-damaging agent methyl methanesulfonate (MMS).
CC {ECO:0000269|PubMed:11598186}.
CC -!- DOMAIN: Subfamily III proteins have a conserved RTxK motif about 40-50
CC residues from the C-terminus; the threonine may be replaced by serine
CC or cysteine. {ECO:0000305|PubMed:27322068}.
CC -!- DISRUPTION PHENOTYPE: Leads to the accumulation of fructose-1-phosphate
CC (PubMed:27322068). Leads to increased DNA damage or decreased repair
CC (PubMed:18085829). {ECO:0000269|PubMed:18085829,
CC ECO:0000269|PubMed:27322068}.
CC -!- MISCELLANEOUS: Present with 6190 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the damage-control phosphatase family. Sugar
CC phosphate phosphatase III subfamily. {ECO:0000305}.
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DR EMBL; Z49211; CAA89130.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA09925.1; -; Genomic_DNA.
DR PIR; S54029; S54029.
DR RefSeq; NP_013740.1; NM_001182523.1.
DR PDB; 3PT1; X-ray; 1.77 A; A=1-470.
DR PDB; 5BY0; X-ray; 1.80 A; A=1-470.
DR PDB; 5F13; X-ray; 2.39 A; A/B/C=1-470.
DR PDBsum; 3PT1; -.
DR PDBsum; 5BY0; -.
DR PDBsum; 5F13; -.
DR AlphaFoldDB; Q04371; -.
DR SMR; Q04371; -.
DR BioGRID; 35199; 46.
DR IntAct; Q04371; 3.
DR MINT; Q04371; -.
DR STRING; 4932.YMR027W; -.
DR iPTMnet; Q04371; -.
DR MaxQB; Q04371; -.
DR PaxDb; Q04371; -.
DR PRIDE; Q04371; -.
DR EnsemblFungi; YMR027W_mRNA; YMR027W; YMR027W.
DR GeneID; 855042; -.
DR KEGG; sce:YMR027W; -.
DR SGD; S000004629; YMR027W.
DR VEuPathDB; FungiDB:YMR027W; -.
DR eggNOG; KOG3870; Eukaryota.
DR GeneTree; ENSGT00530000064023; -.
DR HOGENOM; CLU_030117_2_1_1; -.
DR InParanoid; Q04371; -.
DR OMA; DIKAPWP; -.
DR BioCyc; YEAST:G3O-32732-MON; -.
DR PRO; PR:Q04371; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q04371; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0097023; F:fructose 6-phosphate aldolase activity; IEA:RHEA.
DR GO; GO:0103026; F:fructose-1-phosphatase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016791; F:phosphatase activity; IDA:SGD.
DR GO; GO:2001020; P:regulation of response to DNA damage stimulus; IBA:GO_Central.
DR InterPro; IPR036075; ARMT-1-like_metal-bd_sf.
DR InterPro; IPR039763; ARMT1.
DR InterPro; IPR002791; ARMT1-like_metal-bd.
DR PANTHER; PTHR12260; PTHR12260; 1.
DR Pfam; PF01937; ARMT1-like_dom; 1.
DR SUPFAM; SSF111321; SSF111321; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Manganese; Metal-binding; Nickel;
KW Reference proteome.
FT CHAIN 1..470
FT /note="Damage-control phosphatase YMR027W"
FT /id="PRO_0000203271"
FT MOTIF 420..423
FT /note="Subfamily III RTxK motif"
FT /evidence="ECO:0000305|PubMed:27322068"
FT BINDING 23
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1"
FT BINDING 110
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1"
FT BINDING 254..255
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1"
FT BINDING 254
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1, ECO:0007744|PDB:5BY0"
FT BINDING 255
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1, ECO:0007744|PDB:5BY0"
FT BINDING 292
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1, ECO:0007744|PDB:5BY0"
FT BINDING 384..388
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1"
FT BINDING 423
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:27322068,
FT ECO:0007744|PDB:3PT1"
FT MUTAGEN 110
FT /note="E->A: Strongly reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 114
FT /note="Y->A: Strongly reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 192
FT /note="N->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 254
FT /note="D->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 255
FT /note="N->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 259
FT /note="E->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 263
FT /note="D->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 291
FT /note="S->A: Strongly reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 292
FT /note="D->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 382
FT /note="K->A: Strongly reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 384
FT /note="D->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 420
FT /note="R->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 423
FT /note="K->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT HELIX 15..21
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 23..39
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 47..68
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 77..82
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 106..123
FT /evidence="ECO:0007829|PDB:3PT1"
FT TURN 125..129
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 134..142
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 145..167
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 175..190
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 196..199
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 204..208
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 210..220
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 223..226
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 228..240
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 248..252
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 258..272
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 277..286
FT /evidence="ECO:0007829|PDB:3PT1"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 295..306
FT /evidence="ECO:0007829|PDB:3PT1"
FT TURN 308..310
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 319..336
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 339..344
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 346..349
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 354..356
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 366..373
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 377..382
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 383..391
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 402..405
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 407..410
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 416..421
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 434..443
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 444..446
FT /evidence="ECO:0007829|PDB:3PT1"
FT HELIX 450..455
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 456..458
FT /evidence="ECO:0007829|PDB:3PT1"
FT STRAND 460..465
FT /evidence="ECO:0007829|PDB:3PT1"
SQ SEQUENCE 470 AA; 54129 MW; C71DC2833CF85D5D CRC64;
MTIPGRFMTI DKGTFGEYTA STRWPIIIQN AIDDLSKHQE TEKSNGTKFE QGEVIKKELK
EFRQEIIDRV PLRPFTEEEI KIANVPLSFN EYLKKHPEVN WGAVEWLFSE VYLYRRVNVL
FQRQCEWAKF DIFNRLKQST FESSFYGVVE LALRYENLLP QLREMKQNPG NEIDDILKVL
FKEFIEISLW GNATDLSLLT NATLEDIKSI QGAKARAASE SKIVVNDTEK AWEVLTKARA
DANSREIRVD FVLDNSGFEL YADLMLAAFL LQSGLATKCI FHAKDIPYMV SDVMLKDFDI
LVHDLRDREF FPSGEPSTKE SRALDLFAGE MEKFVSSGKI EFREDSFWTT ELDYWNLDAN
ETKYHGSILH KDLQKSNLVI FKGDLNYRKL TGDRKWPRTT KWETAIGPLA TNGITSLSLR
TCKADVQVAL PEGLDAKLSQ EWEKENPGRG SWWCCSGKWA VICFCSGIHK
