DEOD_BACSU
ID DEOD_BACSU Reviewed; 233 AA.
AC O34925;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Purine nucleoside phosphorylase DeoD-type {ECO:0000255|HAMAP-Rule:MF_01627};
DE Short=PNP {ECO:0000255|HAMAP-Rule:MF_01627};
DE EC=2.4.2.1 {ECO:0000255|HAMAP-Rule:MF_01627};
DE AltName: Full=Purine nucleoside phosphorylase II;
DE Short=PU-NPase II;
GN Name=deoD {ECO:0000255|HAMAP-Rule:MF_01627}; Synonyms=punB;
GN OrderedLocusNames=BSU19630;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9734814; DOI=10.1093/dnares/5.3.195;
RA Ghim S.-Y., Choi S.-K., Shin B.-S., Jeong Y.-M., Sorokin A., Ehrlich S.D.,
RA Park S.-H.;
RT "Sequence analysis of the Bacillus subtilis 168 chromosome region between
RT the sspC and odhA loci (184 degrees-180 degrees).";
RL DNA Res. 5:195-201(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
CC -!- FUNCTION: Catalyzes the reversible phosphorolytic breakdown of the N-
CC glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the
CC formation of the corresponding free purine bases and pentose-1-
CC phosphate. {ECO:0000255|HAMAP-Rule:MF_01627}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a purine D-ribonucleoside + phosphate = a purine nucleobase +
CC alpha-D-ribose 1-phosphate; Xref=Rhea:RHEA:19805, ChEBI:CHEBI:26386,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57720, ChEBI:CHEBI:142355; EC=2.4.2.1;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01627};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a purine 2'-deoxy-D-ribonucleoside + phosphate = 2-deoxy-
CC alpha-D-ribose 1-phosphate + a purine nucleobase;
CC Xref=Rhea:RHEA:36431, ChEBI:CHEBI:26386, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57259, ChEBI:CHEBI:142361; EC=2.4.2.1;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01627};
CC -!- SUBUNIT: Homohexamer; trimer of homodimers. {ECO:0000255|HAMAP-
CC Rule:MF_01627}.
CC -!- SIMILARITY: Belongs to the PNP/UDP phosphorylase family.
CC {ECO:0000255|HAMAP-Rule:MF_01627, ECO:0000305}.
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DR EMBL; AF015775; AAB72065.1; -; Genomic_DNA.
DR EMBL; AF006665; AAB81164.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13854.1; -; Genomic_DNA.
DR PIR; D69614; D69614.
DR RefSeq; NP_389844.1; NC_000964.3.
DR RefSeq; WP_003231176.1; NZ_JNCM01000036.1.
DR PDB; 4D8V; X-ray; 2.35 A; A/B=1-233.
DR PDB; 4D8X; X-ray; 2.65 A; A=1-233.
DR PDB; 4D8Y; X-ray; 1.61 A; A/B/C/D/E/F=1-233.
DR PDB; 4D98; X-ray; 1.70 A; A/B=1-233.
DR PDB; 4D9H; X-ray; 1.91 A; A/B=1-233.
DR PDB; 4DA0; X-ray; 2.95 A; A=1-233.
DR PDB; 4DA6; X-ray; 1.70 A; A=1-233.
DR PDB; 4DA7; X-ray; 2.05 A; A=1-233.
DR PDB; 4DA8; X-ray; 2.60 A; A=1-233.
DR PDB; 4DAB; X-ray; 1.85 A; A=1-233.
DR PDB; 4DAE; X-ray; 2.35 A; A=1-233.
DR PDB; 4DAN; X-ray; 2.56 A; A/B=1-233.
DR PDB; 4DAO; X-ray; 2.22 A; A/B=1-233.
DR PDB; 4DAR; X-ray; 3.15 A; A=1-233.
DR PDBsum; 4D8V; -.
DR PDBsum; 4D8X; -.
DR PDBsum; 4D8Y; -.
DR PDBsum; 4D98; -.
DR PDBsum; 4D9H; -.
DR PDBsum; 4DA0; -.
DR PDBsum; 4DA6; -.
DR PDBsum; 4DA7; -.
DR PDBsum; 4DA8; -.
DR PDBsum; 4DAB; -.
DR PDBsum; 4DAE; -.
DR PDBsum; 4DAN; -.
DR PDBsum; 4DAO; -.
DR PDBsum; 4DAR; -.
DR AlphaFoldDB; O34925; -.
DR SMR; O34925; -.
DR IntAct; O34925; 1.
DR MINT; O34925; -.
DR STRING; 224308.BSU19630; -.
DR jPOST; O34925; -.
DR PaxDb; O34925; -.
DR PRIDE; O34925; -.
DR EnsemblBacteria; CAB13854; CAB13854; BSU_19630.
DR GeneID; 940038; -.
DR KEGG; bsu:BSU19630; -.
DR PATRIC; fig|224308.179.peg.2146; -.
DR eggNOG; COG0813; Bacteria.
DR InParanoid; O34925; -.
DR OMA; PQCLLCG; -.
DR PhylomeDB; O34925; -.
DR BioCyc; BSUB:BSU19630-MON; -.
DR BRENDA; 2.4.2.1; 658.
DR SABIO-RK; O34925; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IBA:GO_Central.
DR GO; GO:0006152; P:purine nucleoside catabolic process; IBA:GO_Central.
DR CDD; cd09006; PNP_EcPNPI-like; 1.
DR Gene3D; 3.40.50.1580; -; 1.
DR HAMAP; MF_01627; Pur_nucleosid_phosp; 1.
DR InterPro; IPR004402; DeoD-type.
DR InterPro; IPR018016; Nucleoside_phosphorylase_CS.
DR InterPro; IPR000845; Nucleoside_phosphorylase_d.
DR InterPro; IPR035994; Nucleoside_phosphorylase_sf.
DR PANTHER; PTHR43691:SF2; PTHR43691:SF2; 1.
DR Pfam; PF01048; PNP_UDP_1; 1.
DR SUPFAM; SSF53167; SSF53167; 1.
DR TIGRFAMs; TIGR00107; deoD; 1.
DR PROSITE; PS01232; PNP_UDP_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosyltransferase; Reference proteome; Transferase.
FT CHAIN 1..233
FT /note="Purine nucleoside phosphorylase DeoD-type"
FT /id="PRO_0000063121"
FT ACT_SITE 203
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT BINDING 4
FT /ligand="a purine D-ribonucleoside"
FT /ligand_id="ChEBI:CHEBI:142355"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT BINDING 20
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT BINDING 24
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT BINDING 43
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT BINDING 87..90
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT BINDING 178..180
FT /ligand="a purine D-ribonucleoside"
FT /ligand_id="ChEBI:CHEBI:142355"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT BINDING 202..203
FT /ligand="a purine D-ribonucleoside"
FT /ligand_id="ChEBI:CHEBI:142355"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P50389"
FT SITE 216
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 14..18
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 22..32
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 47..52
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 66..80
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 84..93
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:4DA0"
FT STRAND 103..112
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 115..120
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 131..144
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 148..155
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 166..171
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 181..190
FT /evidence="ECO:0007829|PDB:4D8Y"
FT STRAND 194..204
FT /evidence="ECO:0007829|PDB:4D8Y"
FT TURN 205..207
FT /evidence="ECO:0007829|PDB:4D8Y"
FT HELIX 213..227
FT /evidence="ECO:0007829|PDB:4D8Y"
FT TURN 228..230
FT /evidence="ECO:0007829|PDB:4D8V"
SQ SEQUENCE 233 AA; 25378 MW; 645FD21146E8F613 CRC64;
MSVHIGAEKG QIADTVLLPG DPLRAKFIAE TYLENVECYN EVRGMYGFTG TYKGKKISVQ
GTGMGVPSIS IYVNELIQSY DVQNLIRVGS CGAIRKDVKV RDVILAMTSS TDSQMNRVAF
GSVDFAPCAD FELLKNAYDA AKDKGVPVTV GSVFTADQFY NDDSQIEKLA KYGVLGVEME
TTALYTLAAK HGRKALSILT VSDHVLTGEE TTAEERQTTF HDMIEVALHS VSQ
