PSUG_ECOLI
ID PSUG_ECOLI Reviewed; 312 AA.
AC P33025; Q2MAR4;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Pseudouridine-5'-phosphate glycosidase {ECO:0000255|HAMAP-Rule:MF_01876, ECO:0000303|PubMed:18591240};
DE Short=PsiMP glycosidase {ECO:0000255|HAMAP-Rule:MF_01876, ECO:0000303|PubMed:18591240};
DE EC=4.2.1.70 {ECO:0000255|HAMAP-Rule:MF_01876, ECO:0000269|PubMed:18591240, ECO:0000269|PubMed:23066817};
GN Name=psuG {ECO:0000255|HAMAP-Rule:MF_01876};
GN Synonyms=pscG, yeiN {ECO:0000303|PubMed:18591240};
GN OrderedLocusNames=b2165, JW2152;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / BHB2600;
RA Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA Church G.M.;
RT "Automated multiplex sequencing of the E.coli genome.";
RL Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=18591240; DOI=10.1074/jbc.m804122200;
RA Preumont A., Snoussi K., Stroobant V., Collet J.-F., Van Schaftingen E.;
RT "Molecular identification of pseudouridine-metabolizing enzymes.";
RL J. Biol. Chem. 283:25238-25246(2008).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF APOENYZME AND COMPLEX WITH
RP D-RIBITOL 5-PHOSPHATE AND WILD-TYPE AND MUTANT ALA-166 IN COMPLEX WITH
RP PSEUDOURIDINE-5'-PHOSPHATE AND MANGANESE, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ACTIVE SITE, REACTION MECHANISM,
RP AND MUTAGENESIS OF GLU-31; LYS-93; ASP-149; LYS-166 AND ASN-289.
RC STRAIN=K12;
RX PubMed=23066817; DOI=10.1021/bi3006829;
RA Huang S., Mahanta N., Begley T.P., Ealick S.E.;
RT "Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.";
RL Biochemistry 51:9245-9255(2012).
CC -!- FUNCTION: Catalyzes the reversible cleavage of pseudouridine 5'-
CC phosphate (PsiMP) to ribose 5-phosphate and uracil. Functions
CC biologically in the cleavage direction, as part of a pseudouridine
CC degradation pathway. {ECO:0000255|HAMAP-Rule:MF_01876,
CC ECO:0000269|PubMed:18591240, ECO:0000269|PubMed:23066817}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribose 5-phosphate + uracil = H2O + psi-UMP;
CC Xref=Rhea:RHEA:18337, ChEBI:CHEBI:15377, ChEBI:CHEBI:17568,
CC ChEBI:CHEBI:58380, ChEBI:CHEBI:78346; EC=4.2.1.70;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01876,
CC ECO:0000269|PubMed:18591240, ECO:0000269|PubMed:23066817};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01876,
CC ECO:0000269|PubMed:18591240, ECO:0000269|PubMed:23066817};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:18591240, ECO:0000269|PubMed:23066817};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:18591240, ECO:0000269|PubMed:23066817};
CC Note=Binds 1 manganese ion per subunit. Can also use Fe(2+) and Co(2+).
CC The unusual metal binding site is heavily hydrated, coordinated with an
CC aspartate side chain and five water molecules, and likely plays a role
CC in anchoring the PsiMP phosphate. {ECO:0000269|PubMed:18591240,
CC ECO:0000269|PubMed:23066817};
CC -!- ACTIVITY REGULATION: Inhibited by Zn(2+) and Ni(2+).
CC {ECO:0000269|PubMed:18591240}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=60 uM for pseudouridine 5'-phosphate (in the presence of 0.5 mM
CC Mn(2+)) {ECO:0000269|PubMed:18591240};
CC KM=169.6 uM for uracil {ECO:0000269|PubMed:23066817};
CC Note=kcat is 3.74 sec(-1) for the synthesis of PsiMP.
CC {ECO:0000269|PubMed:23066817};
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_01876,
CC ECO:0000269|PubMed:23066817}.
CC -!- SIMILARITY: Belongs to the pseudouridine-5'-phosphate glycosidase
CC family. {ECO:0000255|HAMAP-Rule:MF_01876}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U00007; AAA60517.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75226.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76642.1; -; Genomic_DNA.
DR PIR; D64985; D64985.
DR RefSeq; NP_416670.1; NC_000913.3.
DR RefSeq; WP_001292460.1; NZ_LN832404.1.
DR PDB; 4GIJ; X-ray; 1.94 A; A/B/C=1-312.
DR PDB; 4GIK; X-ray; 2.19 A; A/B/C=1-312.
DR PDB; 4GIL; X-ray; 2.54 A; A/B/C=1-312.
DR PDB; 4GIM; X-ray; 1.80 A; A/B/C=1-312.
DR PDBsum; 4GIJ; -.
DR PDBsum; 4GIK; -.
DR PDBsum; 4GIL; -.
DR PDBsum; 4GIM; -.
DR AlphaFoldDB; P33025; -.
DR SMR; P33025; -.
DR BioGRID; 4261702; 6.
DR DIP; DIP-11926N; -.
DR IntAct; P33025; 13.
DR STRING; 511145.b2165; -.
DR jPOST; P33025; -.
DR PaxDb; P33025; -.
DR PRIDE; P33025; -.
DR EnsemblBacteria; AAC75226; AAC75226; b2165.
DR EnsemblBacteria; BAE76642; BAE76642; BAE76642.
DR GeneID; 946699; -.
DR KEGG; ecj:JW2152; -.
DR KEGG; eco:b2165; -.
DR PATRIC; fig|1411691.4.peg.74; -.
DR EchoBASE; EB1968; -.
DR eggNOG; COG2313; Bacteria.
DR HOGENOM; CLU_012201_0_1_6; -.
DR InParanoid; P33025; -.
DR OMA; RKLGHRD; -.
DR PhylomeDB; P33025; -.
DR BioCyc; EcoCyc:EG12033-MON; -.
DR BioCyc; MetaCyc:EG12033-MON; -.
DR BRENDA; 4.2.1.70; 2026.
DR PRO; PR:P33025; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0016798; F:hydrolase activity, acting on glycosyl bonds; IDA:EcoliWiki.
DR GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
DR GO; GO:0004730; F:pseudouridylate synthase activity; IDA:EcoCyc.
DR GO; GO:0046113; P:nucleobase catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.1790.10; -; 1.
DR HAMAP; MF_01876; PsiMP_glycosidase; 1.
DR InterPro; IPR022830; Indigdn_synthA-like.
DR InterPro; IPR007342; PsuG.
DR PANTHER; PTHR42909; PTHR42909; 1.
DR Pfam; PF04227; Indigoidine_A; 1.
DR SUPFAM; SSF110581; SSF110581; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosidase; Hydrolase; Lyase; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..312
FT /note="Pseudouridine-5'-phosphate glycosidase"
FT /id="PRO_0000169150"
FT ACT_SITE 31
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01876,
FT ECO:0000303|PubMed:23066817"
FT ACT_SITE 166
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01876,
FT ECO:0000303|PubMed:23066817"
FT BINDING 93
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01876,
FT ECO:0000269|PubMed:23066817"
FT BINDING 113
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01876,
FT ECO:0000269|PubMed:23066817"
FT BINDING 145
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01876,
FT ECO:0000269|PubMed:23066817"
FT BINDING 147..149
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01876,
FT ECO:0000269|PubMed:23066817"
FT MUTAGEN 31
FT /note="E->A: 7500-fold decrease in reaction rate while
FT little change in substrate affinity."
FT /evidence="ECO:0000269|PubMed:23066817"
FT MUTAGEN 93
FT /note="K->A: 17-fold decrease in reaction rate while modest
FT decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:23066817"
FT MUTAGEN 149
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:23066817"
FT MUTAGEN 166
FT /note="K->A: 2900-fold decrease in reaction rate while no
FT change in substrate affinity."
FT /evidence="ECO:0000269|PubMed:23066817"
FT MUTAGEN 289
FT /note="N->A: 17-fold decrease in reaction rate while modest
FT decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:23066817"
FT TURN 8..10
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 15..22
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 33..36
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 43..57
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 61..68
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 71..75
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:4GIM"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 99..104
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 113..122
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 148..155
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 171..180
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 185..189
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 212..224
FT /evidence="ECO:0007829|PDB:4GIM"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 245..262
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 266..268
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 269..280
FT /evidence="ECO:0007829|PDB:4GIM"
FT TURN 281..283
FT /evidence="ECO:0007829|PDB:4GIM"
FT HELIX 284..310
FT /evidence="ECO:0007829|PDB:4GIM"
SQ SEQUENCE 312 AA; 32910 MW; EBD892C271404F1F CRC64;
MSELKISPEL LQISPEVQDA LKNKKPVVAL ESTIISHGMP FPQNAQTAIE VEETIRKQGA
VPATIAIIGG VMKVGLSKEE IELLGREGHN VTKVSRRDLP FVVAAGKNGA TTVASTMIIA
ALAGIKVFAT GGIGGVHRGA EHTFDISADL QELANTNVTV VCAGAKSILD LGLTTEYLET
FGVPLIGYQT KALPAFFCRT SPFDVSIRLD SASEIARAMV VKWQSGLNGG LVVANPIPEQ
FAMPEHTINA AIDQAVAEAE AQGVIGKEST PFLLARVAEL TGGDSLKSNI QLVFNNAILA
SEIAKEYQRL AG
