ID W9AH10_9BACI Unreviewed; 393 AA.
AC W9AH10;
DT 14-MAY-2014, integrated into UniProtKB/TrEMBL.
DT 14-MAY-2014, sequence version 1.
DT 24-JAN-2024, entry version 48.
DE RecName: Full=Phosphopentomutase {ECO:0000256|HAMAP-Rule:MF_00740};
DE EC=5.4.2.7 {ECO:0000256|HAMAP-Rule:MF_00740};
DE AltName: Full=Phosphodeoxyribomutase {ECO:0000256|HAMAP-Rule:MF_00740};
GN Name=deoB_1 {ECO:0000313|EMBL:CDO01976.1};
GN Synonyms=deoB {ECO:0000256|HAMAP-Rule:MF_00740};
GN ORFNames=BN988_00430 {ECO:0000313|EMBL:CDO01976.1}, OPHB3_1435
GN {ECO:0000313|EMBL:GAQ17510.1};
OS Oceanobacillus picturae.
OC Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Oceanobacillus.
OX NCBI_TaxID=171693 {ECO:0000313|EMBL:CDO01976.1, ECO:0000313|Proteomes:UP000028863};
RN [1] {ECO:0000313|EMBL:CDO01976.1, ECO:0000313|Proteomes:UP000028863}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S1 {ECO:0000313|EMBL:CDO01976.1,
RC ECO:0000313|Proteomes:UP000028863};
RA Croce O., Lagier J.C., Raoult D.;
RT "Draft genome sequencing of Oceanobacillus picturae strain S1 isolated from
RT human gut.";
RL Submitted (MAR-2014) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:CDO01976.1, ECO:0000313|Proteomes:UP000028863}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S1 {ECO:0000313|EMBL:CDO01976.1,
RC ECO:0000313|Proteomes:UP000028863};
RA Urmite Genomes U.;
RL Submitted (MAR-2014) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|Proteomes:UP000052946}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Heshi-B3 {ECO:0000313|Proteomes:UP000052946};
RA Akuzawa S., Nakagawa J., Kanekatsu T., Kanesaki Y., Suzuki T.;
RT "Draft Genome Sequence of Oceanobacillus picturae Heshi-B3 that Was
RT Isolated from Fermented Rice Bran with Aging Salted Mackerel, Which Was
RT Named Heshiko as Traditional Fermented Seafood in Japan.";
RL Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:GAQ17510.1, ECO:0000313|Proteomes:UP000052946}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Heshi-B3 {ECO:0000313|EMBL:GAQ17510.1,
RC ECO:0000313|Proteomes:UP000052946};
RA Akuzawa S., Nagaoka J., Kanekatsu M., Kanesaki Y., Suzuki T.;
RT "Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from
RT Fermented Rice Bran in a Traditional Japanese Seafood Dish.";
RL Genome Announc. 4:e01621-15(2016).
CC -!- FUNCTION: Phosphotransfer between the C1 and C5 carbon atoms of
CC pentose. {ECO:0000256|HAMAP-Rule:MF_00740}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-D-ribose 5-
CC phosphate; Xref=Rhea:RHEA:27658, ChEBI:CHEBI:57259,
CC ChEBI:CHEBI:62877; Evidence={ECO:0000256|HAMAP-Rule:MF_00740};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-D-ribose 1-phosphate = D-ribose 5-phosphate;
CC Xref=Rhea:RHEA:18793, ChEBI:CHEBI:57720, ChEBI:CHEBI:78346;
CC EC=5.4.2.7; Evidence={ECO:0000256|HAMAP-Rule:MF_00740};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00740};
CC Note=Binds 1 or 2 manganese ions. {ECO:0000256|HAMAP-Rule:MF_00740};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose
CC 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from
CC D-ribose 5-phosphate (route II): step 1/3. {ECO:0000256|HAMAP-
CC Rule:MF_00740}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00740}.
CC -!- SIMILARITY: Belongs to the phosphopentomutase family.
CC {ECO:0000256|ARBA:ARBA00010373, ECO:0000256|HAMAP-Rule:MF_00740}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:CDO01976.1}.
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DR EMBL; CCAX010000001; CDO01976.1; -; Genomic_DNA.
DR EMBL; BBXV01000014; GAQ17510.1; -; Genomic_DNA.
DR RefSeq; WP_036572730.1; NZ_QWLU01000001.1.
DR AlphaFoldDB; W9AH10; -.
DR STRING; 171693.BN988_00430; -.
DR eggNOG; COG1015; Bacteria.
DR OrthoDB; 9769930at2; -.
DR UniPathway; UPA00087; UER00173.
DR Proteomes; UP000028863; Unassembled WGS sequence.
DR Proteomes; UP000052946; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008973; F:phosphopentomutase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006015; P:5-phosphoribose 1-diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0043094; P:cellular metabolic compound salvage; IEA:InterPro.
DR GO; GO:0009264; P:deoxyribonucleotide catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd16009; PPM; 1.
DR Gene3D; 3.40.720.10; Alkaline Phosphatase, subunit A; 1.
DR Gene3D; 3.30.70.1250; Phosphopentomutase; 1.
DR HAMAP; MF_00740; Phosphopentomut; 1.
DR InterPro; IPR017850; Alkaline_phosphatase_core_sf.
DR InterPro; IPR010045; DeoB.
DR InterPro; IPR006124; Metalloenzyme.
DR InterPro; IPR024052; Phosphopentomutase_DeoB_cap_sf.
DR NCBIfam; TIGR01696; deoB; 1.
DR PANTHER; PTHR21110; PHOSPHOPENTOMUTASE; 1.
DR PANTHER; PTHR21110:SF0; PHOSPHOPENTOMUTASE; 1.
DR Pfam; PF01676; Metalloenzyme; 1.
DR PIRSF; PIRSF001491; Ppentomutase; 1.
DR SUPFAM; SSF53649; Alkaline phosphatase-like; 1.
DR SUPFAM; SSF143856; DeoB insert domain-like; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00740};
KW Isomerase {ECO:0000256|HAMAP-Rule:MF_00740};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_00740};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00740}; Reference proteome {ECO:0000313|Proteomes:UP000028863}.
FT DOMAIN 5..378
FT /note="Metalloenzyme"
FT /evidence="ECO:0000259|Pfam:PF01676"
FT BINDING 13
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 291
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 327
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 328
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 339
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
SQ SEQUENCE 393 AA; 43725 MW; CC147747C4ED98BB CRC64;
MGNFKRVFLI VMDSVGIGEA PDAEKFNDKG ADTLGHIAEH MNGLKMPNMG SLGLSNIREI
KGINKAEKPK AYYTKMQEAS NGKDTMTGHW EIMGLHIEQP FRTFPEGFPD ELINELEEKS
GRKIIGNKPA SGTEILDELG QEHMDTGALI VYTSADSVLQ IAAHEAIIPI EEQYRICEIA
RELTLDEKYM VGRVIARPFI GSPGAFERTS NRHDYALKPF GHTVMNELQD QKYDVIAIGK
ISDIYDGEGV TEAIRTTDNE DGMTKIVESM DKDFTGISFL NLVDFDAKFG HRRDPKGYGK
ALEAFDSRLP EVLDKMKEDD LLLITADHGN DPVHHGTDHT REYVPLLAYH TGITQATELP
IRKTFADIGA TIAANFEVAT PEHGESFLKD IIN
//
