ID A0A0K0XUK8_9GAMM Unreviewed; 532 AA.
AC A0A0K0XUK8;
DT 11-NOV-2015, integrated into UniProtKB/TrEMBL.
DT 11-NOV-2015, sequence version 1.
DT 27-MAR-2024, entry version 33.
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=HNQ63_001337 {ECO:0000313|EMBL:MBB6086900.1}, WM2015_969
GN {ECO:0000313|EMBL:AKS41350.1};
OS Wenzhouxiangella marina.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales;
OC Wenzhouxiangellaceae; Wenzhouxiangella.
OX NCBI_TaxID=1579979 {ECO:0000313|EMBL:AKS41350.1, ECO:0000313|Proteomes:UP000066624};
RN [1] {ECO:0000313|EMBL:AKS41350.1, ECO:0000313|Proteomes:UP000066624}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KCTC 42284 {ECO:0000313|EMBL:AKS41350.1,
RC ECO:0000313|Proteomes:UP000066624};
RA Noorani M.;
RL Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:MBB6086900.1, ECO:0000313|Proteomes:UP000581413}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 103414 {ECO:0000313|EMBL:MBB6086900.1,
RC ECO:0000313|Proteomes:UP000581413};
RA Goeker M.;
RT "Genomic Encyclopedia of Type Strains, Phase IV (KMG-IV): sequencing the
RT most valuable type-strain genomes for metagenomic binning, comparative
RT biology and taxonomic classification.";
RL Submitted (AUG-2020) 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}.
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DR EMBL; CP012154; AKS41350.1; -; Genomic_DNA.
DR EMBL; JACHIC010000001; MBB6086900.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0K0XUK8; -.
DR STRING; 1579979.WM2015_969; -.
DR KEGG; wma:WM2015_969; -.
DR PATRIC; fig|1579979.3.peg.993; -.
DR OrthoDB; 9769930at2; -.
DR UniPathway; UPA00087; UER00173.
DR Proteomes; UP000066624; Chromosome.
DR Proteomes; UP000581413; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016787; F:hydrolase activity; IEA:InterPro.
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:0008270; F:zinc ion binding; IEA:InterPro.
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; cd01283; cytidine_deaminase; 1.
DR CDD; cd16009; PPM; 1.
DR Gene3D; 3.40.720.10; Alkaline Phosphatase, subunit A; 1.
DR Gene3D; 3.40.140.10; Cytidine Deaminase, domain 2; 1.
DR Gene3D; 3.30.70.1250; Phosphopentomutase; 1.
DR HAMAP; MF_00740; Phosphopentomut; 1.
DR InterPro; IPR017850; Alkaline_phosphatase_core_sf.
DR InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR016193; Cytidine_deaminase-like.
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; PF00383; dCMP_cyt_deam_1; 1.
DR Pfam; PF01676; Metalloenzyme; 1.
DR SUPFAM; SSF53649; Alkaline phosphatase-like; 1.
DR SUPFAM; SSF53927; Cytidine deaminase-like; 1.
DR SUPFAM; SSF143856; DeoB insert domain-like; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00740};
KW Isomerase {ECO:0000256|HAMAP-Rule:MF_00740, ECO:0000313|EMBL:MBB6086900.1};
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:UP000066624};
KW Zinc {ECO:0000256|ARBA:ARBA00022833}.
FT DOMAIN 402..529
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000259|PROSITE:PS51747"
FT BINDING 10
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 305
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 341
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 342
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
FT BINDING 353
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00740"
SQ SEQUENCE 532 AA; 57234 MW; 82572C279880F0EF CRC64;
MPRAIVLVLD SFGIGAAPDA ARFGDAGADT LGHIAAACVS GELDRGPLQL PNLARLGLFH
AHAEATGQVA AGVELIEQPE GAWAHAAERS TGKDTPSGHW ELAGVPVLED FGYFPDKTES
FPEELLEALI RRAELPGVLG NCHASGTEII ERLGAQHIET GKPIVYTSAD SVFQIAAHEE
HFGLDRLYRV CEIARELLMD DRVGRVIARP FVGDVDSGFQ RTGNRRDYSL EPPAPTVLDK
LLDAGGEVLA IGKIGDIFAH RGVSRVIKAD GNEALVDATL AAMDEAGERS LVFTNLVDFD
MLYGHRRDTA GYAAALEAFD RRLPEIIERL RPDDLLILVA DHGCDPSFEG SDHTREFIPV
LALGAGLPAG SLGRRESFAD VGQTLAEHFG LPPMDAGLSF LPLAKARLEQ LHKLRDRAYA
PYSGFTVAAL IETRNGHWFG GCNVETAHYK SVCAEASAIS AMIAAGEREI RRVHILAPGG
RLCAPCGDCR QRLLEFSGPD ARVHLLDNHG MTIEDHAIAE LLPAAFVPDD LD
//
