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Protein

Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase

Gene

phnJ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the breakage of the C-P bond in alpha-D-ribose 1-methylphosphonate 5-phosphate (PRPn) forming alpha-D-ribose 1,2-cyclic phosphate 5-phosphate (PRcP).1 Publication

Catalytic activityi

Alpha-D-ribose 1-methylphosphonate 5-phosphate = alpha-D-ribose 1,2-cyclic phosphate 5-phosphate + methane.1 Publication

Cofactori

Protein has several cofactor binding sites:

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity Source: EcoCyc
  • lyase activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

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

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG10719-MONOMER.
ECOL316407:JW4059-MONOMER.
MetaCyc:EG10719-MONOMER.
RETL1328306-WGS:GSTH-172-MONOMER.
BRENDAi4.7.1.1. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase (EC:4.7.1.1)
Short name:
PRPn C-P lyase
Gene namesi
Name:phnJ
Ordered Locus Names:b4098, JW4059
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10719. phnJ.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 281281Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyasePRO_0000058397Add
BLAST

Proteomic databases

PaxDbiP16688.

Interactioni

Subunit structurei

Forms a complex with PhnG, PhnH, PhnI and PhnK with the suggested composition PhnG4H2I2J2K.1 Publication

Protein-protein interaction databases

BioGridi4263382. 8 interactions.
DIPiDIP-10489N.
IntActiP16688. 4 interactions.
STRINGi511145.b4098.

Structurei

Secondary structure

1
281
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Helixi14 – 2916Combined sources
Helixi50 – 5910Combined sources
Beta strandi65 – 706Combined sources
Helixi77 – 9014Combined sources
Helixi98 – 1003Combined sources
Beta strandi102 – 1087Combined sources
Beta strandi120 – 1245Combined sources
Turni130 – 1345Combined sources
Helixi138 – 14710Combined sources
Helixi151 – 16414Combined sources
Beta strandi175 – 1773Combined sources
Turni178 – 1803Combined sources
Beta strandi181 – 1833Combined sources
Helixi190 – 1967Combined sources
Beta strandi200 – 2078Combined sources
Turni208 – 2114Combined sources
Beta strandi212 – 2165Combined sources
Beta strandi222 – 2243Combined sources
Beta strandi228 – 2303Combined sources
Turni242 – 2443Combined sources
Beta strandi247 – 2493Combined sources
Beta strandi251 – 2555Combined sources
Beta strandi257 – 2604Combined sources
Beta strandi262 – 2687Combined sources
Helixi269 – 2779Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4XB6X-ray1.70D/H1-281[»]
SMRiP16688. Positions 2-278.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the PhnJ family.Curated

Phylogenomic databases

eggNOGiENOG4105FT8. Bacteria.
COG3627. LUCA.
HOGENOMiHOG000147107.
InParanoidiP16688.
KOiK06163.
OMAiFGHIATS.
OrthoDBiEOG6BGNXX.
PhylomeDBiP16688.

Family and domain databases

InterProiIPR010306. PhnJ.
[Graphical view]
PfamiPF06007. PhnJ. 1 hit.
[Graphical view]
PIRSFiPIRSF011468. PhnJ. 1 hit.

Sequencei

Sequence statusi: Complete.

P16688-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MANLSGYNFA YLDEQTKRMI RRAILKAVAI PGYQVPFGGR EMPMPYGWGT
60 70 80 90 100
GGIQLTASVI GESDVLKVID QGADDTTNAV SIRNFFKRVT GVNTTERTDD
110 120 130 140 150
ATVIQTRHRI PETPLTEDQI IIFQVPIPEP LRFIEPRETE TRTMHALEEY
160 170 180 190 200
GVMQVKLYED IARFGHIATT YAYPVKVNGR YVMDPSPIPK FDNPKMDMMP
210 220 230 240 250
ALQLFGAGRE KRIYAVPPFT RVESLDFDDH PFTVQQWDEP CAICGSTHSY
260 270 280
LDEVVLDDAG NRMFVCSDTD YCRQQSEAKN Q
Length:281
Mass (Da):31,845
Last modified:November 1, 1991 - v2
Checksum:i241F6AF140995468
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti103 – 1031V → L in strain: B.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05260 Genomic DNA. Translation: AAA24348.1.
D90227 Genomic DNA. Translation: BAA14270.1.
U14003 Genomic DNA. Translation: AAA96997.1.
U00096 Genomic DNA. Translation: AAC77059.1.
AP009048 Genomic DNA. Translation: BAE78101.1.
PIRiA65219.
RefSeqiNP_418522.1. NC_000913.3.
WP_000002303.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77059; AAC77059; b4098.
BAE78101; BAE78101; BAE78101.
GeneIDi948606.
KEGGiecj:JW4059.
eco:b4098.
PATRICi32123755. VBIEscCol129921_4226.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05260 Genomic DNA. Translation: AAA24348.1.
D90227 Genomic DNA. Translation: BAA14270.1.
U14003 Genomic DNA. Translation: AAA96997.1.
U00096 Genomic DNA. Translation: AAC77059.1.
AP009048 Genomic DNA. Translation: BAE78101.1.
PIRiA65219.
RefSeqiNP_418522.1. NC_000913.3.
WP_000002303.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4XB6X-ray1.70D/H1-281[»]
SMRiP16688. Positions 2-278.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263382. 8 interactions.
DIPiDIP-10489N.
IntActiP16688. 4 interactions.
STRINGi511145.b4098.

Proteomic databases

PaxDbiP16688.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77059; AAC77059; b4098.
BAE78101; BAE78101; BAE78101.
GeneIDi948606.
KEGGiecj:JW4059.
eco:b4098.
PATRICi32123755. VBIEscCol129921_4226.

Organism-specific databases

EchoBASEiEB0713.
EcoGeneiEG10719. phnJ.

Phylogenomic databases

eggNOGiENOG4105FT8. Bacteria.
COG3627. LUCA.
HOGENOMiHOG000147107.
InParanoidiP16688.
KOiK06163.
OMAiFGHIATS.
OrthoDBiEOG6BGNXX.
PhylomeDBiP16688.

Enzyme and pathway databases

BioCyciEcoCyc:EG10719-MONOMER.
ECOL316407:JW4059-MONOMER.
MetaCyc:EG10719-MONOMER.
RETL1328306-WGS:GSTH-172-MONOMER.
BRENDAi4.7.1.1. 2026.

Miscellaneous databases

PROiP16688.

Family and domain databases

InterProiIPR010306. PhnJ.
[Graphical view]
PfamiPF06007. PhnJ. 1 hit.
[Graphical view]
PIRSFiPIRSF011468. PhnJ. 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. "Intermediates in the transformation of phosphonates to phosphate by bacteria."
    Kamat S.S., Williams H.J., Raushel F.M.
    Nature 480:570-573(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR.
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway."
    Jochimsen B., Lolle S., McSorley F.R., Nabi M., Stougaard J., Zechel D.L., Hove-Jensen B.
    Proc. Natl. Acad. Sci. U.S.A. 108:11393-11398(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
    Strain: K12.

Entry informationi

Entry nameiPHNJ_ECOLI
AccessioniPrimary (citable) accession number: P16688
Secondary accession number(s): Q2M6K5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: November 1, 1991
Last modified: March 16, 2016
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The sequence shown is that of strain K12.

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
  3. SIMILARITY comments
    Index of protein domains and families

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.