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Protein

Phosphoribosyl 1,2-cyclic phosphodiesterase

Gene

phnP

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of the cyclic ribose-phosphate to form alpha-D-ribose 1,5-bisphosphate.2 Publications

Catalytic activityi

5-phospho-alpha-D-ribose 1,2-cyclic phosphate + H2O = alpha-D-ribose 1,5-bisphosphate.1 Publication

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi21 – 211Zinc2 Publications
Metal bindingi23 – 231Zinc2 Publications
Metal bindingi26 – 261Zinc2 Publications
Metal bindingi76 – 761Manganese 1; via tele nitrogen2 Publications
Metal bindingi78 – 781Manganese 1; via pros nitrogen2 Publications
Metal bindingi80 – 801Manganese 22 Publications
Metal bindingi81 – 811Manganese 2; via tele nitrogen2 Publications
Metal bindingi143 – 1431Manganese 1; via tele nitrogen2 Publications
Metal bindingi164 – 1641Manganese 12 Publications
Metal bindingi164 – 1641Manganese 22 Publications
Metal bindingi222 – 2221Manganese 2; via tele nitrogen2 Publications
Metal bindingi225 – 2251Zinc; via pros nitrogen2 Publications

GO - Molecular functioni

  • manganese ion binding Source: EcoCyc
  • phosphoric diester hydrolase activity Source: EcoCyc

GO - Biological processi

  • organic phosphonate catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Manganese, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10725-MONOMER.
ECOL316407:JW4053-MONOMER.
MetaCyc:EG10725-MONOMER.
BRENDAi3.1.4.55. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphoribosyl 1,2-cyclic phosphodiesterase (EC:3.1.4.55)
Alternative name(s):
Phosphoribosyl cyclic phosphodiesterase
Gene namesi
Name:phnP
Ordered Locus Names:b4092, JW4053
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10725. phnP.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi54 – 541D → A: Has a 1000-fold lower activity. 1 Publication
Mutagenesisi75 – 751T → A: Has 40-fold lower activity. 1 Publication
Mutagenesisi78 – 781H → A: Has 250-fold lower activity. 1 Publication
Mutagenesisi80 – 801D → A: Has 1000-fold lower activity, and has 100-fold lower affinity for manganese. 1 Publication
Mutagenesisi164 – 1641D → A: Has a 1000-fold lower activity. 1 Publication
Mutagenesisi187 – 1871D → A: No effect. 1 Publication
Mutagenesisi200 – 2001H → A: Has 10-fold lower activity. 1 Publication
Mutagenesisi222 – 2221H → A: Has 9-fold lower activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 252252Phosphoribosyl 1,2-cyclic phosphodiesterasePRO_0000058402Add
BLAST

Proteomic databases

PaxDbiP16692.
PRIDEiP16692.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

BioGridi4261542. 7 interactions.
IntActiP16692. 1 interaction.
STRINGi511145.b4092.

Structurei

Secondary structure

1
252
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Helixi24 – 318Combined sources
Helixi33 – 353Combined sources
Beta strandi39 – 468Combined sources
Beta strandi49 – 535Combined sources
Helixi60 – 634Combined sources
Beta strandi71 – 733Combined sources
Helixi79 – 824Combined sources
Helixi83 – 853Combined sources
Turni86 – 905Combined sources
Beta strandi92 – 943Combined sources
Beta strandi96 – 1005Combined sources
Turni108 – 1125Combined sources
Beta strandi117 – 1226Combined sources
Beta strandi129 – 1313Combined sources
Beta strandi134 – 1407Combined sources
Beta strandi143 – 1453Combined sources
Beta strandi148 – 1536Combined sources
Beta strandi158 – 1625Combined sources
Helixi170 – 1789Combined sources
Beta strandi182 – 1876Combined sources
Beta strandi190 – 1923Combined sources
Beta strandi198 – 2003Combined sources
Helixi203 – 21311Combined sources
Beta strandi218 – 2225Combined sources
Helixi225 – 2317Combined sources
Beta strandi240 – 2423Combined sources
Beta strandi247 – 2493Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3G1PX-ray1.40A/B1-252[»]
3P2UX-ray1.48A/B1-252[»]
ProteinModelPortaliP16692.
SMRiP16692. Positions 13-251.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16692.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4107SA6. Bacteria.
COG1235. LUCA.
HOGENOMiHOG000223791.
InParanoidiP16692.
KOiK06167.
OMAiPRNHNDL.
OrthoDBiEOG6VF33T.
PhylomeDBiP16692.

Family and domain databases

Gene3Di3.60.15.10. 1 hit.
InterProiIPR001279. Metallo-B-lactamas.
IPR017693. Phosphonate_metab_PhnP.
[Graphical view]
PfamiPF12706. Lactamase_B_2. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
TIGRFAMsiTIGR03307. PhnP. 1 hit.

Sequencei

Sequence statusi: Complete.

P16692-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLTLTLTGT GGAQGVPAWG CECAACARAR RSPQYRRQPC SGVVKFNDAI
60 70 80 90 100
TLIDAGLHDL ADRWSPGSFQ QFLLTHYHMD HVQGLFPLRW GVGDPIPVYG
110 120 130 140 150
PPDEQGCDDL FKHPGLLDFS HTVEPFVVFD LQGLQVTPLP LNHSKLTFGY
160 170 180 190 200
LLETAHSRVA WLSDTAGLPE KTLKFLRNNQ PQVMVMDCSH PPRADAPRNH
210 220 230 240 250
CDLNTVLALN QVIRSPRVIL THISHQFDAW LMENALPSGF EVGFDGMEIG

VA
Length:252
Mass (Da):27,848
Last modified:August 1, 1990 - v1
Checksum:iE23922C46A8386F5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05260 Genomic DNA. Translation: AAA24356.1.
D90227 Genomic DNA. Translation: BAA14276.1.
U14003 Genomic DNA. Translation: AAA96991.1.
U00096 Genomic DNA. Translation: AAC77053.1.
AP009048 Genomic DNA. Translation: BAE78095.1.
PIRiH35719.
RefSeqiNP_418516.1. NC_000913.3.
WP_000059908.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77053; AAC77053; b4092.
BAE78095; BAE78095; BAE78095.
GeneIDi948600.
KEGGiecj:JW4053.
eco:b4092.
PATRICi32123743. VBIEscCol129921_4220.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05260 Genomic DNA. Translation: AAA24356.1.
D90227 Genomic DNA. Translation: BAA14276.1.
U14003 Genomic DNA. Translation: AAA96991.1.
U00096 Genomic DNA. Translation: AAC77053.1.
AP009048 Genomic DNA. Translation: BAE78095.1.
PIRiH35719.
RefSeqiNP_418516.1. NC_000913.3.
WP_000059908.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3G1PX-ray1.40A/B1-252[»]
3P2UX-ray1.48A/B1-252[»]
ProteinModelPortaliP16692.
SMRiP16692. Positions 13-251.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261542. 7 interactions.
IntActiP16692. 1 interaction.
STRINGi511145.b4092.

Proteomic databases

PaxDbiP16692.
PRIDEiP16692.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77053; AAC77053; b4092.
BAE78095; BAE78095; BAE78095.
GeneIDi948600.
KEGGiecj:JW4053.
eco:b4092.
PATRICi32123743. VBIEscCol129921_4220.

Organism-specific databases

EchoBASEiEB0719.
EcoGeneiEG10725. phnP.

Phylogenomic databases

eggNOGiENOG4107SA6. Bacteria.
COG1235. LUCA.
HOGENOMiHOG000223791.
InParanoidiP16692.
KOiK06167.
OMAiPRNHNDL.
OrthoDBiEOG6VF33T.
PhylomeDBiP16692.

Enzyme and pathway databases

BioCyciEcoCyc:EG10725-MONOMER.
ECOL316407:JW4053-MONOMER.
MetaCyc:EG10725-MONOMER.
BRENDAi3.1.4.55. 2026.

Miscellaneous databases

EvolutionaryTraceiP16692.
PROiP16692.

Family and domain databases

Gene3Di3.60.15.10. 1 hit.
InterProiIPR001279. Metallo-B-lactamas.
IPR017693. Phosphonate_metab_PhnP.
[Graphical view]
PfamiPF12706. Lactamase_B_2. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
TIGRFAMsiTIGR03307. PhnP. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B."
    Chen C.-M., Ye Q.-Z., Zhu Z., Wanner B.L., Walsh C.T.
    J. Biol. Chem. 265:4461-4471(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: B.
  2. "Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12."
    Makino K., Kim S.K., Shinagawa H., Amemura M., Nakata A.
    J. Bacteriol. 173:2665-2672(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway."
    Hove-Jensen B., McSorley F.R., Zechel D.L.
    J. Am. Chem. Soc. 133:3617-3624(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  7. "Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation."
    Podzelinska K., He S.M., Wathier M., Yakunin A., Proudfoot M., Hove-Jensen B., Zechel D.L., Jia Z.
    J. Biol. Chem. 284:17216-17226(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) IN COMPLEX WITH MANGANESE; ZINC AND S-MALATE, FUNCTION, COFACTOR, SUBUNIT, SUBSTRATE SPECIFICITY, MUTAGENESIS OF ASP-80.
  8. "Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway."
    He S.M., Wathier M., Podzelinska K., Wong M., McSorley F.R., Asfaw A., Hove-Jensen B., Jia Z., Zechel D.L.
    Biochemistry 50:8603-8615(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) IN COMPLEX WITH MANGANESE; ZINC AND ORTHOVANADATE, MUTAGENESIS OF ASP-54; THR-75; HIS-78; ASP-164; ASP-187; HIS-200 AND HIS-222, ENZYME KINETICS.

Entry informationi

Entry nameiPHNP_ECOLI
AccessioniPrimary (citable) accession number: P16692
Secondary accession number(s): Q2M6L1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: May 11, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The sequence shown is that of strains K12 and B.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.