DEOD1_VIBCH
ID DEOD1_VIBCH Reviewed; 241 AA.
AC Q9KPM0;
DT 24-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Purine nucleoside phosphorylase DeoD-type 1 {ECO:0000255|HAMAP-Rule:MF_01627};
DE Short=PNP 1 {ECO:0000255|HAMAP-Rule:MF_01627};
DE EC=2.4.2.1 {ECO:0000255|HAMAP-Rule:MF_01627};
GN Name=deoD1 {ECO:0000255|HAMAP-Rule:MF_01627}; OrderedLocusNames=VC_2347;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) OF 2-241 IN COMPLEX WITH ADENOSINE.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS) IN COMPLEX WITH PHOSPHATE.
RA Kim J., Ramagopal U.A., Burley S.K., Almo S.C.;
RT "Crystal structure of PNP with an inhibitor DADME_immH from Vibrio
RT cholerae.";
RL Submitted (AUG-2010) to the PDB data bank.
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}.
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DR EMBL; AE003852; AAF95490.1; -; Genomic_DNA.
DR PIR; C82087; C82087.
DR RefSeq; NP_231977.1; NC_002505.1.
DR RefSeq; WP_000224887.1; NZ_LT906614.1.
DR PDB; 1VHJ; X-ray; 2.23 A; A/B/C/D/E/F=2-241.
DR PDB; 1VHW; X-ray; 1.54 A; A/B/C/D/E/F=2-241.
DR PDB; 3OF3; X-ray; 1.83 A; A/B/C/D/E/F/G/H/I/J/K/L=1-241.
DR PDBsum; 1VHJ; -.
DR PDBsum; 1VHW; -.
DR PDBsum; 3OF3; -.
DR AlphaFoldDB; Q9KPM0; -.
DR SMR; Q9KPM0; -.
DR STRING; 243277.VC_2347; -.
DR DNASU; 2613143; -.
DR EnsemblBacteria; AAF95490; AAF95490; VC_2347.
DR GeneID; 57990740; -.
DR GeneID; 66939815; -.
DR KEGG; vch:VC_2347; -.
DR PATRIC; fig|243277.26.peg.2234; -.
DR eggNOG; COG0813; Bacteria.
DR HOGENOM; CLU_068457_2_0_6; -.
DR OMA; PQCLLCG; -.
DR BioCyc; VCHO:VC2347-MON; -.
DR EvolutionaryTrace; Q9KPM0; -.
DR Proteomes; UP000000584; Chromosome 1.
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..241
FT /note="Purine nucleoside phosphorylase DeoD-type 1"
FT /id="PRO_0000063169"
FT ACT_SITE 205
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT BINDING 5
FT /ligand="a purine D-ribonucleoside"
FT /ligand_id="ChEBI:CHEBI:142355"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0007744|PDB:1VHW"
FT BINDING 21
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:0007744|PDB:3OF3"
FT BINDING 25
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:0007744|PDB:3OF3"
FT BINDING 44
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0007744|PDB:3OF3"
FT BINDING 88..91
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:0007744|PDB:3OF3"
FT BINDING 180..182
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:0007744|PDB:1VHW"
FT BINDING 204..205
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 218
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01627"
FT STRAND 15..19
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 23..33
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 34..41
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 67..81
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 85..94
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 104..113
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 116..120
FT /evidence="ECO:0007829|PDB:1VHW"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 132..144
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 166..173
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 183..193
FT /evidence="ECO:0007829|PDB:1VHW"
FT STRAND 196..206
FT /evidence="ECO:0007829|PDB:1VHW"
FT TURN 207..209
FT /evidence="ECO:0007829|PDB:1VHW"
FT HELIX 215..237
FT /evidence="ECO:0007829|PDB:1VHW"
SQ SEQUENCE 241 AA; 26124 MW; 6E55A07972166241 CRC64;
MATPHINAQM GDFADVVLMP GDPLRAKYIA ENFLDNAVQV CDVRNMFGYT GTYKGRKISV
MGHGMGIPSC SIYVTELIKD YGVKKIIRVG SCGAVNEGIK VRDVVIGMGA CTDSKVNRIR
FKDHDFAAIA DYKMVKAAEE AAKARGIDVK VGNLFSAELF YTPDPSMFDV MDKYGIVGVE
MEAAGIYGVA AEYGAKALAI CTVSDHIKTG EQTTSEERQN TFNEMIEIAL DSVLIGDQAG
Y
