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Database: UniProt
Entry: A0A0J8VDN0_9GAMM
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ID   A0A0J8VDN0_9GAMM        Unreviewed;       406 AA.
AC   A0A0J8VDN0;
DT   14-OCT-2015, integrated into UniProtKB/TrEMBL.
DT   14-OCT-2015, sequence version 1.
DT   24-JAN-2024, entry version 41.
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 {ECO:0000256|HAMAP-Rule:MF_00740};
GN   ORFNames=C9I94_12765 {ECO:0000313|EMBL:PSW24201.1};
OS   Photobacterium swingsii.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Photobacterium.
OX   NCBI_TaxID=680026 {ECO:0000313|EMBL:PSW24201.1, ECO:0000313|Proteomes:UP000240481};
RN   [1] {ECO:0000313|EMBL:PSW24201.1, ECO:0000313|Proteomes:UP000240481}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 24669 {ECO:0000313|EMBL:PSW24201.1,
RC   ECO:0000313|Proteomes:UP000240481};
RA   Butler K.;
RT   "Whole genome sequencing of Histamine producing bacteria.";
RL   Submitted (JAN-2018) to the EMBL/GenBank/DDBJ databases.
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:PSW24201.1}.
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DR   EMBL; PYLZ01000006; PSW24201.1; -; Genomic_DNA.
DR   RefSeq; WP_048898034.1; NZ_PYLZ01000006.1.
DR   AlphaFoldDB; A0A0J8VDN0; -.
DR   STRING; 680026.AB733_06510; -.
DR   OrthoDB; 9769930at2; -.
DR   UniPathway; UPA00087; UER00173.
DR   Proteomes; UP000240481; 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}.
FT   DOMAIN          2..396
FT                   /note="Metalloenzyme"
FT                   /evidence="ECO:0000259|Pfam:PF01676"
FT   BINDING         10
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT   BINDING         310
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT   BINDING         346
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT   BINDING         347
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT   BINDING         358
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
SQ   SEQUENCE   406 AA;  43913 MW;  0CE4721424B65578 CRC64;
     MKRSIILVLD SFGIGATEDA VNFGDVGANT MGHIAQACAR GEADNGERSG PLHLPNLNKL
     GLGKACEESS GYFPEGLDAQ VEITGAYGHA KELSSGKDTP SGHWEIAGVP VLFDWGYFTD
     HSNSFPQELL DSIVERANLP GYLGNCHASG TQVLDDLGEE HMKTGKPIFY TSADSVFQIA
     CHEETYGLDN LLALCQIVRE ELEDYNIGRV IARPFVGAGK GQFERTGNRR DLSVEPPAPT
     VLQKLVEEKN GDVISIGKIS DIYAGCGITK KVKATGIPDL FDATLEQIKQ AGDNSLVFTN
     FVDFDSAYGH RRNVAGYAAA LEYFDKRLPE VLELLQEDDV LVLTADHGCD PTWEGTDHTR
     EHIPVIVTGP KVAAGSLGRR ETFADIGQSL AAHHGLTDMD YGKSFL
//
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