PPDE_DEIRA
ID PPDE_DEIRA Reviewed; 255 AA.
AC Q9RUV0;
DT 12-APR-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Phosphatase/phosphodiesterase DR_1281 {ECO:0000305};
DE AltName: Full=2',3'-cyclic-nucleotide 2'-phosphodiesterase {ECO:0000305};
DE EC=3.1.4.16 {ECO:0000269|PubMed:17847097};
DE AltName: Full=Calcineurin-like phosphoesterase {ECO:0000303|PubMed:17847097};
DE AltName: Full=Phosphoenolpyruvate phosphatase {ECO:0000305};
DE EC=3.1.3.60 {ECO:0000269|PubMed:17847097};
GN OrderedLocusNames=DR_1281 {ECO:0000312|EMBL:AAF10852.1};
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2] {ECO:0007744|PDB:1T70}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17847097; DOI=10.1002/prot.21584;
RA Shin D.H., Proudfoot M., Lim H.J., Choi I.K., Yokota H., Yakunin A.F.,
RA Kim R., Kim S.H.;
RT "Structural and enzymatic characterization of DR1281: A calcineurin-like
RT phosphoesterase from Deinococcus radiodurans.";
RL Proteins 70:1000-1009(2008).
CC -!- FUNCTION: Has a dual activity phosphatase/phosphodiesterase in vitro,
CC with a preference to phosphoenolpyruvate (PEP) and 2',3'-cAMP,
CC respectively. Can also use 2',3'-cGMP, 2',3'-cCMP and various model
CC substrates such as p-nitrophenyl phosphate (pNPP), bis-p-nitrophenyl
CC phosphate (bis-pNPP) and p-nitrophenyl thymidine monophosphate (pNP-
CC TMP). {ECO:0000269|PubMed:17847097}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a nucleoside 2',3'-cyclic phosphate + H2O = a nucleoside 3'-
CC phosphate + H(+); Xref=Rhea:RHEA:19621, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:66949, ChEBI:CHEBI:66954; EC=3.1.4.16;
CC Evidence={ECO:0000269|PubMed:17847097};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + phosphoenolpyruvate = phosphate + pyruvate;
CC Xref=Rhea:RHEA:19997, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58702; EC=3.1.3.60;
CC Evidence={ECO:0000269|PubMed:17847097};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:17847097};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:17847097};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:17847097};
CC Note=Mn(2+) is the preferable metal for phosphatase activity.
CC Phosphodiesterase activity is observed in the presence of Co(2+),
CC Mn(2+) or Fe(2+). {ECO:0000269|PubMed:17847097};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.36 mM for PEP (at pH 6.5) {ECO:0000269|PubMed:17847097};
CC KM=0.55 mM for 2',3'-cAMP (at pH 6.5) {ECO:0000269|PubMed:17847097};
CC KM=0.87 mM for 2',3'-cCMP (at pH 6.5) {ECO:0000269|PubMed:17847097};
CC KM=1.28 mM for 2',3'-cGMP (at pH 6.5) {ECO:0000269|PubMed:17847097};
CC KM=0.08 mM for pNPP (at pH 8.5) {ECO:0000269|PubMed:17847097};
CC KM=0.22 mM for bis-pNPP (at pH 8.5) {ECO:0000269|PubMed:17847097};
CC KM=0.05 mM for pNP-TMP (at pH 8.5) {ECO:0000269|PubMed:17847097};
CC Vmax=0.38 umol/min/mg enzyme with PEP as substrate (at pH 6.5)
CC {ECO:0000269|PubMed:17847097};
CC Vmax=0.83 umol/min/mg enzyme with 2',3'-cAMP as substrate (at pH 6.5)
CC {ECO:0000269|PubMed:17847097};
CC Vmax=0.68 umol/min/mg enzyme with 2',3'-cCMP as substrate (at pH 6.5)
CC {ECO:0000269|PubMed:17847097};
CC Vmax=0.91 umol/min/mg enzyme with 2',3'-cGMP as substrate (at pH 6.5)
CC {ECO:0000269|PubMed:17847097};
CC Vmax=0.44 umol/min/mg enzyme with pNPP as substrate (at pH 8.5)
CC {ECO:0000269|PubMed:17847097};
CC Vmax=13.8 umol/min/mg enzyme with bis-pNPP as substrate (at pH 8.5)
CC {ECO:0000269|PubMed:17847097};
CC Vmax=2.79 umol/min/mg enzyme with pNP-TMP as substrate (at pH 8.5)
CC {ECO:0000269|PubMed:17847097};
CC Note=kcat is 0.18 sec(-1) with PEP as substrate. kcat is 0.38 sec(-1)
CC with 2',3'-cAMP as substrate. kcat is 0.32 sec(-1) with 2',3'-cCMP as
CC substrate. kcat is 0.42 sec(-1) with 2',3'-cGMP as substrate. kcat is
CC 0.20 sec(-1) with pNPP as substrate. kcat is 6.97 sec(-1) with bis-
CC pNPP as substrate. kcat is 1.41 sec(-1) with pNP-TMP as substrate.
CC {ECO:0000269|PubMed:17847097};
CC pH dependence:
CC Optimum pH is 6.0-7.0. {ECO:0000269|PubMed:17847097};
CC -!- SIMILARITY: Belongs to the YmdB-like family. {ECO:0000305}.
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DR EMBL; AE000513; AAF10852.1; -; Genomic_DNA.
DR PIR; D75415; D75415.
DR RefSeq; NP_295005.1; NC_001263.1.
DR RefSeq; WP_010887924.1; NZ_CP015081.1.
DR PDB; 1T70; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-255.
DR PDBsum; 1T70; -.
DR AlphaFoldDB; Q9RUV0; -.
DR SMR; Q9RUV0; -.
DR STRING; 243230.DR_1281; -.
DR EnsemblBacteria; AAF10852; AAF10852; DR_1281.
DR KEGG; dra:DR_1281; -.
DR PATRIC; fig|243230.17.peg.1477; -.
DR eggNOG; COG1692; Bacteria.
DR HOGENOM; CLU_068238_0_0_0; -.
DR InParanoid; Q9RUV0; -.
DR OMA; NHIWDKK; -.
DR OrthoDB; 1127353at2; -.
DR EvolutionaryTrace; Q9RUV0; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0008663; F:2',3'-cyclic-nucleotide 2'-phosphodiesterase activity; IEA:UniProtKB-EC.
DR GO; GO:0004113; F:2',3'-cyclic-nucleotide 3'-phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050189; F:phosphoenolpyruvate phosphatase activity; IEA:UniProtKB-EC.
DR Gene3D; 3.60.21.10; -; 1.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR005235; YmdB-like.
DR PANTHER; PTHR36303; PTHR36303; 1.
DR Pfam; PF13277; YmdB; 1.
DR PIRSF; PIRSF004789; DR1281; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Hydrolase; Iron; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..255
FT /note="Phosphatase/phosphodiesterase DR_1281"
FT /id="PRO_0000439640"
FT ACT_SITE 66
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 8
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 37
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 37
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 38
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 65
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 148
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 173
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT BINDING 175
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O31775"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 11..25
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:1T70"
FT TURN 39..42
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 47..56
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:1T70"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 73..78
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 106..116
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 127..134
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 165..174
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:1T70"
FT TURN 185..187
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 197..203
FT /evidence="ECO:0007829|PDB:1T70"
FT HELIX 209..217
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 230..240
FT /evidence="ECO:0007829|PDB:1T70"
FT STRAND 243..253
FT /evidence="ECO:0007829|PDB:1T70"
SQ SEQUENCE 255 AA; 27936 MW; 82F9DB08AD169D46 CRC64;
MRVLFIGDVF GQPGRRVLQN HLPTIRPQFD FVIVNMENSA GGFGMHRDAA RGALEAGAGC
LTLGNHAWHH KDIYPMLSED TYPIVRPLNY ADPGTPGVGW RTFDVNGEKL TVVNLLGRVF
MEAVDNPFRT MDALLERDDL GTVFVDFHAE ATSEKEAMGW HLAGRVAAVI GTHTHVPTAD
TRILKGGTAY QTDAGFTGPH DSIIGSAIEG PLQRFLTERP HRYGVAEGRA ELNGVALHFE
GGKATAAERY RFIED
