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Escherichia coli K-12 substr. MG1655 Enzyme: 5-phospho-α-D-ribosyl 1,2-cyclic phosphate phosphodiesterase

Gene: phnP Accession Numbers: EG10725 (EcoCyc), b4092, ECK4085

Regulation Summary Diagram: ?

Regulation summary diagram for phnP

Subunit composition of 5-phospho-α-D-ribosyl 1,2-cyclic phosphate phosphodiesterase = [PhnP]2
         5-phospho-α-D-ribosyl 1,2-cyclic phosphate phosphodiesterase = PhnP

PhnP is a 5-phospho-α-D-ribosyl 1,2-cyclic phosphate phosphodiesterase. 5-phospho-α-D-ribosyl 1,2-cyclic phosphate is an intermediate in the catabolism of organophosphonates [HoveJensen11]. Phosphodiesterase activity towards bis(p-nitrophenyl)phosphate and 2',3'-cyclic nucleotides was first shown by [Podzelinska09]. The pathway for the catabolism of phosphonates has been elucidated [Kamat11].

phnP is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90a, Metcalf93a].

Crystal structures of PhnP have been solved [Podzelinska08, Podzelinska09, He11]. The H200 residue was thought to provide the general acid for catalysis; however, results from site-directed mutagenesis of that residue indicate a different role. An alternate reaction mechanism has been proposed [He11].

Gene Citations: [Wanner92, Metcalf93]

Locations: cytosol

Map Position: [4,312,367 <- 4,313,125] (92.95 centisomes, 335°)
Length: 759 bp / 252 aa

Molecular Weight of Polypeptide: 27.848 kD (from nucleotide sequence)

Molecular Weight of Multimer: 44.5 kD (experimental) [Podzelinska09]

Unification Links: ASAP:ABE-0013412 , CGSC:34514 , EchoBASE:EB0719 , EcoGene:EG10725 , EcoliWiki:b4092 , ModBase:P16692 , OU-Microarray:b4092 , PortEco:phnP , PR:PRO_000023539 , Pride:P16692 , Protein Model Portal:P16692 , RefSeq:NP_418516 , RegulonDB:EG10725 , SMR:P16692 , String:511145.b4092 , UniProt:P16692

Relationship Links: InterPro:IN-FAMILY:IPR001279 , InterPro:IN-FAMILY:IPR017693 , Panther:IN-FAMILY:PTHR12553:SF21 , PDB:Structure:3G1P , PDB:Structure:3P2U , Smart:IN-FAMILY:SM00849

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for phnP

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment Inferred by computational analysis [GOA01, Metcalf93a]
Molecular Function: GO:0008081 - phosphoric diester hydrolase activity Inferred from experiment Inferred by computational analysis [GOA01, Podzelinska09]
GO:0030145 - manganese ion binding Inferred from experiment [Podzelinska09]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Essentiality data for phnP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Curated 09-Mar-2006 by Shearer A , SRI International
Revised 08-Jul-2011 by Keseler I , SRI International
Last-Curated ? 19-Dec-2011 by Keseler I , SRI International

Enzymatic reaction of: 5-phospho-α-D-ribosyl 1,2-cyclic phosphate phosphodiesterase

EC Number:

5-phospho-α-D-ribose 1,2-cyclic phosphate + H2O <=> α-D-ribose 1,5-bisphosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for 5-phospho-α-D-ribose 1,2-cyclic phosphate: a nucleoside 2',3'-cyclic phosphate [Podzelinska09 ]

In Pathways: methylphosphonate degradation I

Cofactors or Prosthetic Groups: Mn2+ [Podzelinska09]

pH(opt): 7 [BRENDA14, He11], 7.2 [BRENDA14, Podzelinska09]

Sequence Features

Protein sequence of 5-phospho-alpha-D-ribosyl 1,2-cyclic phosphate phosphodiesterase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 21
[He11, Podzelinska09, UniProt15]
UniProt: Zinc.
Metal-Binding-Site 23
[He11, Podzelinska09, UniProt15]
UniProt: Zinc.
Metal-Binding-Site 26
[He11, Podzelinska09, UniProt15]
UniProt: Zinc.
Mutagenesis-Variant 54
[He11, UniProt13]
UniProt: Has a 1000-fold lower activity.
Mutagenesis-Variant 75
[He11, UniProt13]
UniProt: Has 40-fold lower activity.
Metal-Binding-Site 76
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 1; via tele nitrogen.
Metal-Binding-Site 78
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 1; via pros nitrogen.
Mutagenesis-Variant 78
[He11, UniProt13]
UniProt: Has 250-fold lower activity.
Metal-Binding-Site 80
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 2.
Mutagenesis-Variant 80
[Podzelinska09, UniProt13]
UniProt: Has 1000-fold lower activity, and has 100-fold lower affinity for manganese.
Metal-Binding-Site 81
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 2; via tele nitrogen.
Metal-Binding-Site 143
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 1; via tele nitrogen.
Metal-Binding-Site 164
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 1.
Mutagenesis-Variant 164
[He11, UniProt13]
UniProt: Has a 1000-fold lower activity.
Mutagenesis-Variant 187
[He11, UniProt13]
UniProt: No effect.
Mutagenesis-Variant 200
[He11, UniProt13]
UniProt: Has 10-fold lower activity.
Metal-Binding-Site 222
[He11, Podzelinska09, UniProt15]
UniProt: Manganese 2; via tele nitrogen.
Mutagenesis-Variant 222
[He11, UniProt13]
UniProt: Has 9-fold lower activity.
Metal-Binding-Site 225
[He11, Podzelinska09, UniProt15]
UniProt: Zinc; via pros nitrogen.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4092 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10725; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Chen90a: Chen CM, Ye QZ, Zhu ZM, Wanner BL, Walsh CT (1990). "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." J Biol Chem 265(8);4461-71. PMID: 2155230

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

He11: He SM, Wathier M, Podzelinska K, Wong M, McSorley FR, Asfaw A, Hove-Jensen B, Jia Z, Zechel DL (2011). "Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway." Biochemistry 50(40);8603-15. PMID: 21830807

HoveJensen11: Hove-Jensen B, McSorley FR, Zechel DL (2011). "Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway." J Am Chem Soc 133(10);3617-24. PMID: 21341651

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kamat11: Kamat SS, Williams HJ, Raushel FM (2011). "Intermediates in the transformation of phosphonates to phosphate by bacteria." Nature 480(7378);570-3. PMID: 22089136

Metcalf91: Metcalf WW, Wanner BL (1991). "Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi." J Bacteriol 1991;173(2);587-600. PMID: 1846145

Metcalf93: Metcalf WW, Wanner BL (1993). "Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements." J Bacteriol 175(11);3430-42. PMID: 8388873

Metcalf93a: Metcalf WW, Wanner BL (1993). "Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli." Gene 129(1);27-32. PMID: 8335257

Podzelinska08: Podzelinska K, He S, Soares A, Zechel D, Hove-Jensen B, Jia Z (2008). "Expression, purification and preliminary diffraction studies of PhnP." Acta Crystallogr Sect F Struct Biol Cryst Commun 64(Pt 6);554-7. PMID: 18540074

Podzelinska09: Podzelinska K, He SM, Wathier M, Yakunin A, Proudfoot M, Hove-Jensen B, Zechel DL, Jia Z (2009). "Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation." J Biol Chem 284(25);17216-26. PMID: 19366688

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wanner92: Wanner BL, Metcalf WW (1992). "Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation." FEMS Microbiol Lett 79(1-3);133-9. PMID: 1335942

Yakovleva98: Yakovleva GM, Kim SK, Wanner BL (1998). "Phosphate-independent expression of the carbon-phosphorus lyase activity of Escherichia coli." Appl Microbiol Biotechnol 49(5);573-8. PMID: 9650256

Other References Related to Gene Regulation

Jiang95: Jiang W, Metcalf WW, Lee KS, Wanner BL (1995). "Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2." J Bacteriol 1995;177(22);6411-21. PMID: 7592415

Makino91: Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A (1991). "Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12." J Bacteriol 1991;173(8);2665-12. PMID: 1840580

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Wanner90: Wanner BL, Boline JA (1990). "Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli." J Bacteriol 172(3);1186-96. PMID: 2155195

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Sep 1, 2015, BIOCYC14B.