PHNP_ECOLI
ID PHNP_ECOLI Reviewed; 252 AA.
AC P16692; Q2M6L1;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase;
DE EC=3.1.4.55;
DE AltName: Full=Phosphoribosyl cyclic phosphodiesterase;
GN Name=phnP; OrderedLocusNames=b4092, JW4053;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=B;
RX PubMed=2155230; DOI=10.1016/s0021-9258(19)39587-0;
RA Chen C.-M., Ye Q.-Z., Zhu Z., Wanner B.L., Walsh C.T.;
RT "Molecular biology of carbon-phosphorus bond cleavage. Cloning and
RT sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and
RT C-P lyase activity in Escherichia coli B.";
RL J. Biol. Chem. 265:4461-4471(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1840580; DOI=10.1128/jb.173.8.2665-2672.1991;
RA Makino K., Kim S.K., Shinagawa H., Amemura M., Nakata A.;
RT "Molecular analysis of the cryptic and functional phn operons for
RT phosphonate use in Escherichia coli K-12.";
RL J. Bacteriol. 173:2665-2672(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=21341651; DOI=10.1021/ja1102713;
RA Hove-Jensen B., McSorley F.R., Zechel D.L.;
RT "Physiological role of phnP-specified phosphoribosyl cyclic
RT phosphodiesterase in catabolism of organophosphonic acids by the carbon-
RT phosphorus lyase pathway.";
RL J. Am. Chem. Soc. 133:3617-3624(2011).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) IN COMPLEX WITH MANGANESE; ZINC AND
RP S-MALATE, FUNCTION, COFACTOR, SUBUNIT, SUBSTRATE SPECIFICITY, AND
RP MUTAGENESIS OF ASP-80.
RX PubMed=19366688; DOI=10.1074/jbc.m808392200;
RA Podzelinska K., He S.M., Wathier M., Yakunin A., Proudfoot M.,
RA Hove-Jensen B., Zechel D.L., Jia Z.;
RT "Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase
RT pathway for phosphonate degradation.";
RL J. Biol. Chem. 284:17216-17226(2009).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) IN COMPLEX WITH MANGANESE; ZINC AND
RP ORTHOVANADATE, MUTAGENESIS OF ASP-54; THR-75; HIS-78; ASP-164; ASP-187;
RP HIS-200 AND HIS-222, AND ENZYME KINETICS.
RX PubMed=21830807; DOI=10.1021/bi2005398;
RA He S.M., Wathier M., Podzelinska K., Wong M., McSorley F.R., Asfaw A.,
RA Hove-Jensen B., Jia Z., Zechel D.L.;
RT "Structure and mechanism of PhnP, a phosphodiesterase of the carbon-
RT phosphorus lyase pathway.";
RL Biochemistry 50:8603-8615(2011).
CC -!- FUNCTION: Catalyzes the hydrolysis of the cyclic ribose-phosphate to
CC form alpha-D-ribose 1,5-bisphosphate. {ECO:0000269|PubMed:19366688,
CC ECO:0000269|PubMed:21341651}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-D-ribose 1,2-cyclic phosphate 5-phosphate + H2O = alpha-
CC D-ribose 1,5-bisphosphate + H(+); Xref=Rhea:RHEA:34795,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:68687,
CC ChEBI:CHEBI:68688; EC=3.1.4.55;
CC Evidence={ECO:0000269|PubMed:21341651};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:19366688};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000269|PubMed:19366688};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:19366688};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:19366688};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19366688,
CC ECO:0000269|PubMed:21830807}.
CC -!- MISCELLANEOUS: The sequence shown is that of strains K12 and B.
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DR EMBL; J05260; AAA24356.1; -; Genomic_DNA.
DR EMBL; D90227; BAA14276.1; -; Genomic_DNA.
DR EMBL; U14003; AAA96991.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77053.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78095.1; -; Genomic_DNA.
DR PIR; H35719; H35719.
DR RefSeq; NP_418516.1; NC_000913.3.
DR RefSeq; WP_000059908.1; NZ_SSUW01000018.1.
DR PDB; 3G1P; X-ray; 1.40 A; A/B=1-252.
DR PDB; 3P2U; X-ray; 1.48 A; A/B=1-252.
DR PDBsum; 3G1P; -.
DR PDBsum; 3P2U; -.
DR AlphaFoldDB; P16692; -.
DR SMR; P16692; -.
DR BioGRID; 4261542; 14.
DR IntAct; P16692; 1.
DR STRING; 511145.b4092; -.
DR jPOST; P16692; -.
DR PaxDb; P16692; -.
DR PRIDE; P16692; -.
DR EnsemblBacteria; AAC77053; AAC77053; b4092.
DR EnsemblBacteria; BAE78095; BAE78095; BAE78095.
DR GeneID; 948600; -.
DR KEGG; ecj:JW4053; -.
DR KEGG; eco:b4092; -.
DR PATRIC; fig|1411691.4.peg.2608; -.
DR EchoBASE; EB0719; -.
DR eggNOG; COG1235; Bacteria.
DR HOGENOM; CLU_044538_3_0_6; -.
DR InParanoid; P16692; -.
DR OMA; HIHFDHL; -.
DR PhylomeDB; P16692; -.
DR BioCyc; EcoCyc:EG10725-MON; -.
DR BioCyc; MetaCyc:EG10725-MON; -.
DR BRENDA; 3.1.4.55; 2026.
DR EvolutionaryTrace; P16692; -.
DR PRO; PR:P16692; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0103043; F:5-phospho-alpha-D-ribosyl 1,2-cyclic phosphate phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
DR GO; GO:0019700; P:organic phosphonate catabolic process; IMP:EcoCyc.
DR CDD; cd07736; PhnP-like_MBL-fold; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR035682; PhnP_MBL.
DR InterPro; IPR017693; Phosphonate_metab_PhnP.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR Pfam; PF12706; Lactamase_B_2; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR TIGRFAMs; TIGR03307; PhnP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Manganese; Metal-binding; Reference proteome;
KW Zinc.
FT CHAIN 1..252
FT /note="Phosphoribosyl 1,2-cyclic phosphate
FT phosphodiesterase"
FT /id="PRO_0000058402"
FT BINDING 21
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 23
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 26
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 76
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 78
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 80
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 81
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 143
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 164
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 164
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 222
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT BINDING 225
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19366688,
FT ECO:0000269|PubMed:21830807"
FT MUTAGEN 54
FT /note="D->A: Has a 1000-fold lower activity."
FT /evidence="ECO:0000269|PubMed:21830807"
FT MUTAGEN 75
FT /note="T->A: Has 40-fold lower activity."
FT /evidence="ECO:0000269|PubMed:21830807"
FT MUTAGEN 78
FT /note="H->A: Has 250-fold lower activity."
FT /evidence="ECO:0000269|PubMed:21830807"
FT MUTAGEN 80
FT /note="D->A: Has 1000-fold lower activity, and has 100-fold
FT lower affinity for manganese."
FT /evidence="ECO:0000269|PubMed:19366688"
FT MUTAGEN 164
FT /note="D->A: Has a 1000-fold lower activity."
FT /evidence="ECO:0000269|PubMed:21830807"
FT MUTAGEN 187
FT /note="D->A: No effect."
FT /evidence="ECO:0000269|PubMed:21830807"
FT MUTAGEN 200
FT /note="H->A: Has 10-fold lower activity."
FT /evidence="ECO:0000269|PubMed:21830807"
FT MUTAGEN 222
FT /note="H->A: Has 9-fold lower activity."
FT /evidence="ECO:0000269|PubMed:21830807"
FT STRAND 3..9
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 24..31
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 39..46
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 49..53
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:3G1P"
FT TURN 86..90
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 96..100
FT /evidence="ECO:0007829|PDB:3G1P"
FT TURN 108..112
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 117..122
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 129..131
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 158..162
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 170..178
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 182..187
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 203..213
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:3G1P"
FT HELIX 225..231
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 240..242
FT /evidence="ECO:0007829|PDB:3G1P"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:3G1P"
SQ SEQUENCE 252 AA; 27848 MW; E23922C46A8386F5 CRC64;
MSLTLTLTGT GGAQGVPAWG CECAACARAR RSPQYRRQPC SGVVKFNDAI TLIDAGLHDL
ADRWSPGSFQ QFLLTHYHMD HVQGLFPLRW GVGDPIPVYG PPDEQGCDDL FKHPGLLDFS
HTVEPFVVFD LQGLQVTPLP LNHSKLTFGY LLETAHSRVA WLSDTAGLPE KTLKFLRNNQ
PQVMVMDCSH PPRADAPRNH CDLNTVLALN QVIRSPRVIL THISHQFDAW LMENALPSGF
EVGFDGMEIG VA
