PURNU_GEOS3
ID PURNU_GEOS3 Reviewed; 274 AA.
AC P84138; A0A0K2H5Q6;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 17-JUN-2020, sequence version 2.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Purine nucleoside phosphorylase YlmD {ECO:0000305};
DE EC=2.4.2.1 {ECO:0000269|PubMed:31978345};
DE AltName: Full=Adenosine deaminase YlmD {ECO:0000305};
DE EC=3.5.4.4 {ECO:0000269|PubMed:31978345};
DE AltName: Full=S-methyl-5'-thioadenosine phosphorylase YlmD {ECO:0000305};
DE EC=2.4.2.28 {ECO:0000269|PubMed:31978345};
GN Name=ylmD {ECO:0000303|PubMed:31978345};
OS Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=272567;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 13240 / CIP 106956 / 10;
RA Lewis S.A., Clifton S.W., Najar F.Z., Roe B.A.;
RT "Complete genome Sequence of Geobacillus stearothermophilus strain 10, a
RT Yellowstone hot spring isolate.";
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ZINC.
RA Minasov G., Shuvalova L., Mondragon A., Taneja B., Moy S.F., Collart F.R.,
RA Anderson W.F.;
RT "1.8 A crystal structure of an uncharacterized B. stearothermophilus
RT protein.";
RL Submitted (MAY-2004) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) IN COMPLEX WITH ZINC AND INOSINE,
RP FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=31978345; DOI=10.1016/j.cell.2019.12.017;
RA Cader M.Z., de Almeida Rodrigues R.P., West J.A., Sewell G.W.,
RA Md-Ibrahim M.N., Reikine S., Sirago G., Unger L.W., Inglesias-Romero A.B.,
RA Ramshorn K., Haag L.M., Saveljeva S., Ebel J.F., Rosenstiel P.,
RA Kaneider N.C., Lee J.C., Lawley T.D., Bradley A., Dougan G., Modis Y.,
RA Griffin J.L., Kaser A.;
RT "FAMIN is a multifunctional purine enzyme enabling the purine nucleotide
RT cycle.";
RL Cell 180:278-295(2020).
CC -!- FUNCTION: Purine nucleoside enzyme that catalyzes the phosphorolysis of
CC adenosine and inosine nucleosides, yielding D-ribose 1-phosphate and
CC the respective free bases, adenine and hypoxanthine (PubMed:31978345).
CC Also catalyzes the phosphorolysis of S-methyl-5'-thioadenosine into
CC adenine and S-methyl-5-thio-alpha-D-ribose 1-phosphate
CC (PubMed:31978345). Also has adenosine deaminase activity
CC (PubMed:31978345). {ECO:0000269|PubMed:31978345}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate;
CC Xref=Rhea:RHEA:27642, ChEBI:CHEBI:16335, ChEBI:CHEBI:16708,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57720; EC=2.4.2.1;
CC Evidence={ECO:0000269|PubMed:31978345};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27643;
CC Evidence={ECO:0000269|PubMed:31978345};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + S-methyl-5'-thioadenosine = adenine + S-methyl-5-
CC thio-alpha-D-ribose 1-phosphate; Xref=Rhea:RHEA:11852,
CC ChEBI:CHEBI:16708, ChEBI:CHEBI:17509, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58533; EC=2.4.2.28;
CC Evidence={ECO:0000269|PubMed:31978345};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:11853;
CC Evidence={ECO:0000269|PubMed:31978345};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=inosine + phosphate = alpha-D-ribose 1-phosphate +
CC hypoxanthine; Xref=Rhea:RHEA:27646, ChEBI:CHEBI:17368,
CC ChEBI:CHEBI:17596, ChEBI:CHEBI:43474, ChEBI:CHEBI:57720; EC=2.4.2.1;
CC Evidence={ECO:0000269|PubMed:31978345};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27647;
CC Evidence={ECO:0000269|PubMed:31978345};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine + H(+) + H2O = inosine + NH4(+);
CC Xref=Rhea:RHEA:24408, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16335, ChEBI:CHEBI:17596, ChEBI:CHEBI:28938; EC=3.5.4.4;
CC Evidence={ECO:0000269|PubMed:31978345};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24409;
CC Evidence={ECO:0000269|PubMed:31978345};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:31978345};
CC Note=Binds 2 zinc ions (PubMed:31978345). One zinc is catalytic and
CC mediates binding to the substrate, while the second is probably
CC structural (PubMed:31978345). {ECO:0000269|PubMed:31978345};
CC -!- SIMILARITY: Belongs to the purine nucleoside phosphorylase YfiH/LACC1
CC family. {ECO:0000305}.
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DR EMBL; CP008934; ALA69258.1; -; Genomic_DNA.
DR RefSeq; WP_053413740.1; NZ_CP008934.1.
DR PDB; 1T8H; X-ray; 1.80 A; A=1-274.
DR PDB; 6T0Y; X-ray; 1.20 A; A=1-274.
DR PDB; 6T1B; X-ray; 1.20 A; A=1-274.
DR PDBsum; 1T8H; -.
DR PDBsum; 6T0Y; -.
DR PDBsum; 6T1B; -.
DR AlphaFoldDB; P84138; -.
DR SMR; P84138; -.
DR EnsemblBacteria; ALA69258; ALA69258; GT50_02955.
DR KEGG; gse:GT50_02955; -.
DR PATRIC; fig|272567.8.peg.600; -.
DR EvolutionaryTrace; P84138; -.
DR GO; GO:0004000; F:adenosine deaminase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IDA:UniProtKB.
DR GO; GO:0017061; F:S-methyl-5-thioadenosine phosphorylase activity; IDA:UniProtKB.
DR CDD; cd16833; YfiH; 1.
DR Gene3D; 3.60.140.10; -; 1.
DR InterPro; IPR003730; Cu_polyphenol_OxRdtase.
DR InterPro; IPR038371; Cu_polyphenol_OxRdtase_sf.
DR InterPro; IPR011324; Cytotoxic_necrot_fac-like_cat.
DR PANTHER; PTHR30616; PTHR30616; 1.
DR Pfam; PF02578; Cu-oxidase_4; 1.
DR SUPFAM; SSF64438; SSF64438; 1.
DR TIGRFAMs; TIGR00726; TIGR00726; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Transferase; Zinc.
FT CHAIN 1..274
FT /note="Purine nucleoside phosphorylase YlmD"
FT /id="PRO_0000449802"
FT BINDING 46..47
FT /ligand="inosine"
FT /ligand_id="ChEBI:CHEBI:17596"
FT /evidence="ECO:0000269|PubMed:31978345,
FT ECO:0007744|PDB:6T1B"
FT BINDING 80
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:31978345,
FT ECO:0007744|PDB:6T1B"
FT BINDING 125
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:31978345,
FT ECO:0007744|PDB:6T1B"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:31978345,
FT ECO:0007744|PDB:6T1B"
FT BINDING 182
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:31978345, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:1T8H, ECO:0007744|PDB:6T0Y,
FT ECO:0007744|PDB:6T1B"
FT BINDING 183
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:31978345, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:1T8H, ECO:0007744|PDB:6T0Y,
FT ECO:0007744|PDB:6T1B"
FT BINDING 242
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:31978345, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:1T8H, ECO:0007744|PDB:6T0Y,
FT ECO:0007744|PDB:6T1B"
FT BINDING 245
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:31978345, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:1T8H, ECO:0007744|PDB:6T0Y,
FT ECO:0007744|PDB:6T1B"
FT BINDING 262
FT /ligand="inosine"
FT /ligand_id="ChEBI:CHEBI:17596"
FT /evidence="ECO:0000269|PubMed:31978345,
FT ECO:0007744|PDB:6T1B"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 9..15
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 18..20
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 52..66
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:6T0Y"
FT TURN 92..96
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 107..115
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 117..132
FT /evidence="ECO:0007829|PDB:6T0Y"
FT TURN 133..136
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:6T0Y"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 188..194
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 205..210
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 218..228
FT /evidence="ECO:0007829|PDB:6T0Y"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:6T0Y"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:6T0Y"
FT TURN 247..249
FT /evidence="ECO:0007829|PDB:6T0Y"
FT TURN 253..258
FT /evidence="ECO:0007829|PDB:6T0Y"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:6T0Y"
SQ SEQUENCE 274 AA; 29844 MW; 3EA6DC81021FD440 CRC64;
MPDIFQQEAR GWLRCGAPPF AGAVAGLTTK HGGESKGPFA SLNMGLHVGD DRTDVVNNRR
RLAEWLAFPL ERWVCCEQVH GADIQKVTKS DRGNGAQDFA TAVPGVDGLY TDEAGVLLAL
CFADCVPIYF VAPSAGLVGL AHAGWRGTAG GIAGHMVWLW QTREHIAPSD IYVAIGPAIG
PCCYTVDDRV VDSLRPTLPP ESPLPWRETS PGQYALDLKE ANRLQLLAAG VPNSHIYVSE
RCTSCEEALF FSHRRDRGTT GRMLAFIGRR EEWT
