DEOB_BACCR
ID DEOB_BACCR Reviewed; 394 AA.
AC Q818Z9;
DT 28-NOV-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Phosphopentomutase {ECO:0000255|HAMAP-Rule:MF_00740};
DE EC=5.4.2.7 {ECO:0000255|HAMAP-Rule:MF_00740};
DE AltName: Full=Phosphodeoxyribomutase {ECO:0000255|HAMAP-Rule:MF_00740};
GN Name=deoB {ECO:0000255|HAMAP-Rule:MF_00740}; OrderedLocusNames=BC_4087;
OS Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC
OS 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=226900;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373
RC / NCTC 2599 / NRRL B-3711;
RX PubMed=12721630; DOI=10.1038/nature01582;
RA Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V.,
RA Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M.,
RA Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch G.,
RA Haselkorn R., Fonstein M., Ehrlich S.D., Overbeek R., Kyrpides N.C.;
RT "Genome sequence of Bacillus cereus and comparative analysis with Bacillus
RT anthracis.";
RL Nature 423:87-91(2003).
CC -!- FUNCTION: Phosphotransfer between the C1 and C5 carbon atoms of
CC pentose. {ECO:0000255|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:0000255|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; EC=5.4.2.7; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00740};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00740};
CC Note=Binds 1 or 2 manganese ions. {ECO:0000255|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:0000255|HAMAP-
CC Rule:MF_00740}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00740}.
CC -!- SIMILARITY: Belongs to the phosphopentomutase family.
CC {ECO:0000255|HAMAP-Rule:MF_00740}.
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DR EMBL; AE016877; AAP11006.1; -; Genomic_DNA.
DR RefSeq; NP_833805.1; NC_004722.1.
DR RefSeq; WP_001046079.1; NZ_CP034551.1.
DR PDB; 3M8W; X-ray; 1.85 A; A/B/C=2-394.
DR PDB; 3M8Y; X-ray; 2.10 A; A/B/C=2-394.
DR PDB; 3M8Z; X-ray; 1.80 A; A/B/C=2-394.
DR PDB; 3OT9; X-ray; 1.75 A; A/B/C=2-394.
DR PDB; 3TWZ; X-ray; 1.75 A; A=2-394.
DR PDB; 3TX0; X-ray; 2.26 A; A=2-394.
DR PDB; 3UN2; X-ray; 1.80 A; A/B/C=2-394.
DR PDB; 3UN3; X-ray; 1.80 A; A/B/C=2-394.
DR PDB; 3UN5; X-ray; 1.80 A; A/B/C/D/E/F=2-394.
DR PDB; 3UNY; X-ray; 1.95 A; A/B/C/D/E/F=2-394.
DR PDB; 3UO0; X-ray; 2.30 A; A/B/C=2-394.
DR PDB; 4LR7; X-ray; 2.10 A; A/B/C=2-394.
DR PDB; 4LR8; X-ray; 2.00 A; A/B/C=2-394.
DR PDB; 4LR9; X-ray; 2.10 A; A/B/C=2-394.
DR PDB; 4LRA; X-ray; 2.00 A; A/B/C=2-394.
DR PDB; 4LRB; X-ray; 2.00 A; A/B/C=2-394.
DR PDB; 4LRC; X-ray; 1.89 A; A/B/C=2-394.
DR PDB; 4LRD; X-ray; 1.78 A; A=2-394.
DR PDB; 4LRE; X-ray; 2.10 A; A/B/C=2-394.
DR PDB; 4LRF; X-ray; 2.00 A; A/B/C=2-394.
DR PDBsum; 3M8W; -.
DR PDBsum; 3M8Y; -.
DR PDBsum; 3M8Z; -.
DR PDBsum; 3OT9; -.
DR PDBsum; 3TWZ; -.
DR PDBsum; 3TX0; -.
DR PDBsum; 3UN2; -.
DR PDBsum; 3UN3; -.
DR PDBsum; 3UN5; -.
DR PDBsum; 3UNY; -.
DR PDBsum; 3UO0; -.
DR PDBsum; 4LR7; -.
DR PDBsum; 4LR8; -.
DR PDBsum; 4LR9; -.
DR PDBsum; 4LRA; -.
DR PDBsum; 4LRB; -.
DR PDBsum; 4LRC; -.
DR PDBsum; 4LRD; -.
DR PDBsum; 4LRE; -.
DR PDBsum; 4LRF; -.
DR AlphaFoldDB; Q818Z9; -.
DR SMR; Q818Z9; -.
DR STRING; 226900.BC_4087; -.
DR EnsemblBacteria; AAP11006; AAP11006; BC_4087.
DR GeneID; 67508725; -.
DR KEGG; bce:BC4087; -.
DR PATRIC; fig|226900.8.peg.4222; -.
DR HOGENOM; CLU_053861_0_0_9; -.
DR OMA; YLGNCHA; -.
DR BRENDA; 5.4.2.7; 648.
DR UniPathway; UPA00087; UER00173.
DR EvolutionaryTrace; Q818Z9; -.
DR Proteomes; UP000001417; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IBA:GO_Central.
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; 3.30.70.1250; -; 1.
DR Gene3D; 3.40.720.10; -; 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 PANTHER; PTHR21110; PTHR21110; 1.
DR Pfam; PF01676; Metalloenzyme; 1.
DR PIRSF; PIRSF001491; Ppentomutase; 1.
DR SUPFAM; SSF143856; SSF143856; 1.
DR SUPFAM; SSF53649; SSF53649; 1.
DR TIGRFAMs; TIGR01696; deoB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isomerase; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..394
FT /note="Phosphopentomutase"
FT /id="PRO_0000199807"
FT BINDING 13
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00740"
FT BINDING 291
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00740"
FT BINDING 327
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00740"
FT BINDING 328
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00740"
FT BINDING 339
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00740"
FT STRAND 5..12
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 23..26
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 33..40
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 47..52
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 54..57
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 70..76
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 85..92
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 110..120
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 124..129
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 132..146
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 155..164
FT /evidence="ECO:0007829|PDB:3OT9"
FT TURN 165..167
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 170..183
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 187..189
FT /evidence="ECO:0007829|PDB:3TWZ"
FT STRAND 192..202
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 224..230
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 241..244
FT /evidence="ECO:0007829|PDB:3OT9"
FT TURN 245..249
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 251..254
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 259..270
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 275..282
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 284..288
FT /evidence="ECO:0007829|PDB:3OT9"
FT TURN 289..293
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 295..306
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 309..315
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 320..325
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 327..329
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 332..338
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 344..349
FT /evidence="ECO:0007829|PDB:3OT9"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 367..377
FT /evidence="ECO:0007829|PDB:3OT9"
FT HELIX 389..391
FT /evidence="ECO:0007829|PDB:3OT9"
SQ SEQUENCE 394 AA; 44020 MW; 0B1E0804BC5FFAD2 CRC64;
MNKYKRIFLV VMDSVGIGEA PDAEQFGDLG SDTIGHIAEH MNGLQMPNMV KLGLGNIREM
KGISKVEKPL GYYTKMQEKS TGKDTMTGHW EIMGLYIDTP FQVFPEGFPK ELLDELEEKT
GRKIIGNKPA SGTEILDELG QEQMETGSLI VYTSADSVLQ IAAHEEVVPL DELYKICKIA
RELTLDEKYM VGRVIARPFV GEPGNFTRTP NRHDYALKPF GRTVMNELKD SDYDVIAIGK
ISDIYDGEGV TESLRTKSNM DGMDKLVDTL NMDFTGLSFL NLVDFDALFG HRRDPQGYGE
ALQEYDARLP EVFAKLKEDD LLLITADHGN DPIHPGTDHT REYVPLLAYS PSMKEGGQEL
PLRQTFADIG ATVAENFGVK MPEYGTSFLN ELKK
