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O34313 (NTPES_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 97. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Trifunctional nucleotide phosphoesterase protein YfkN

Including the following 2 domains:

  1. 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
    EC=3.1.3.6
    EC=3.1.4.16
  2. 5'-nucleotidase
    EC=3.1.3.5
Gene names
Name:yfkN
Ordered Locus Names:BSU07840
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length1462 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the release of inorganic phosphate from 2',3'-cyclic nucleotides through consecutive 2',3'-phosphodiesterase and 3'- (or 2') nucleotidase activities. Also possesses a 5'-nucleotidase activity. Does not catalyze the release of inorganic phosphate from 3',5'-cyclic nucleotides. Probably plays a role in the cellular reprocessing of nucleotides present in the medium, under conditions of phosphate shortage. Ref.3

Catalytic activity

Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate. Ref.3

A 3'-ribonucleotide + H2O = a ribonucleoside + phosphate. Ref.3

A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate. Ref.3

Cofactor

Divalent cations By similarity.

Subcellular location

Secretedcell wall; Peptidoglycan-anchor Probable Ref.3.

Induction

Expression is induced in response to phosphate starvation in a PhoR-dependent manner. Ref.4

Domain

The N-terminal region (amino acids 35-623) is able to catalyze the release of phosphate from 2',3'-cyclic nucleotides, but not from 5'-nucleotides. Ref.3

Sequence similarities

Belongs to the 5'-nucleotidase family.

Biophysicochemical properties

Kinetic parameters:

The 2',3'-cyclic phosphodiesterase activity is higher than that of the 5'-nucleotidase with the four major nucleotides used as substrates. Ref.3

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3535 Ref.3
Chain36 – 14271392Trifunctional nucleotide phosphoesterase protein YfkN
PRO_0000390884
Propeptide1428 – 146235Removed by sortase Potential
PRO_0000390885

Regions

Region36 – 6235882',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase
Region561 – 56773'-ribonucleotide binding By similarity
Region624 – 14278045'-nucleotidase
Region1127 – 113375'-ribonucleotide binding By similarity
Motif1424 – 14285LPXTG sorting signal Potential

Sites

Metal binding521Divalent metal cation 1
Metal binding541Divalent metal cation 1
Metal binding971Divalent metal cation 1
Metal binding971Divalent metal cation 2
Metal binding1411Divalent metal cation 2
Metal binding2491Divalent metal cation 2
Metal binding2821Divalent metal cation 2
Metal binding2841Divalent metal cation 1
Metal binding6761Divalent metal cation 3 By similarity
Metal binding6781Divalent metal cation 3 By similarity
Metal binding7081Divalent metal cation 3 By similarity
Metal binding7081Divalent metal cation 4 By similarity
Metal binding7401Divalent metal cation 4 By similarity
Metal binding8721Divalent metal cation 4 By similarity
Metal binding8951Divalent metal cation 4 By similarity
Metal binding8971Divalent metal cation 3 By similarity
Binding site45813'-ribonucleotide By similarity
Binding site104715'-ribonucleotide By similarity

Amino acid modifications

Modified residue14271Pentaglycyl murein peptidoglycan amidated threonine Potential

Secondary structure

........................................................ 1462
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O34313 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: EE769201F34DA84C

FASTA1,462159,706
        10         20         30         40         50         60 
MRIQKRRTHV ENILRILLPP IMILSLILPT PPIHAEESAA PQVHLSILAT TDIHANMMDY 

        70         80         90        100        110        120 
DYYSDKETAD FGLARTAQLI QKHREQNPNT LLVDNGDLIQ GNPLGEYAVK YQKDDIISGT 

       130        140        150        160        170        180 
KTHPIISVMN ALKYDAGTLG NHEFNYGLDF LDGTIKGADF PIVNANVKTT SGENRYTPYV 

       190        200        210        220        230        240 
INEKTLIDEN GNEQKVKVGY IGFVPPQIMT WDKKNLEGQV QVQDIVESAN ETIPKMKAEG 

       250        260        270        280        290        300 
ADVIIALAHT GIEKQAQSSG AENAVFDLAT KTKGIDAIIS GHQHGLFPSA EYAGVAQFNV 

       310        320        330        340        350        360 
EKGTINGIPV VMPSSWGKYL GVIDLKLEKA DGSWKVADSK GSIESIAGNV TSRNETVTNT 

       370        380        390        400        410        420 
IQQTHQNTLE YVRKPVGKTE ADINSFFAQV KDDPSIQIVT DAQKWYAEKE MKDTEYKNLP 

       430        440        450        460        470        480 
ILSAGAPFKA GGRNGANYYT NIPAGDLAIK NVGDLYLYDN TVQIVKLTGS EVKDWLEMSA 

       490        500        510        520        530        540 
GQFNQIDPAK GGDQALLNEN FRSYNFDVID GVTYQVDVTK PAKYNENGKV INADSSRIIN 

       550        560        570        580        590        600 
LSYEGKPISP SQEFLVVTNN YRASGGGGFP HLTSDKIVHG SAVENRQVLM DYIIEQKTVN 

       610        620        630        640        650        660 
PKADNNWSIA PVSGTNLTFE SSLLAKPFAD KADDVAYVGK SANEGYGVYK LQFDDDSNPD 

       670        680        690        700        710        720 
PPKDGLWDLT VMHTNDTHAH LDDAARRMTK INEVRSETNH NILLDAGDVF SGDLYFTKWN 

       730        740        750        760        770        780 
GLADLKMMNM MGYDAMTFGN HEFDKGPTVL SDFLSGNSAT VDPANRYHFE APEFPIVSAN 

       790        800        810        820        830        840 
VDVSNEPKLK SFVKKPQTFT AGEKKEAGIH PYILLDVDGE KVAVFGLTTE DTATTSSPGK 

       850        860        870        880        890        900 
SIVFNDAFET AQNTVKAIQE EEKVNKIIAL THIGHNRDLE LAKKVKGIDL IIGGHTHTLV 

       910        920        930        940        950        960 
DKMEVVNNEE PTIVAQAKEY GQFLGRVDVA FDEKGVVQTD KSNLSVLPID EHTEENPEAK 

       970        980        990       1000       1010       1020 
QELDQFKNEL EDVKNEKVGY TDVALDGQRE HVRTKETNLG NFIADGMLAK AKEAAGARIA 

      1030       1040       1050       1060       1070       1080 
ITNGGGIRAG IDKGDITLGE VLNVMPFGNT LYVADLTGKQ IKEALEQGLS NVENGGGAFP 

      1090       1100       1110       1120       1130       1140 
QVAGIEYTFT LNNKPGHRVL EVKIESPNGD KVAINTDDTY RVATNNFVGA GGDGYSVFTE 

      1150       1160       1170       1180       1190       1200 
ASHGEDLGYV DYEIFTEQLK KLGNKVSPKV EGRIKEVFLP TKQKDGSWTL DEDKFAIYAK 

      1210       1220       1230       1240       1250       1260 
NANTPFVYYG IHEGSQEKPI NLKVKKDQVK LLKERESDPS LTMFNYWYSM KMPMANLKTA 

      1270       1280       1290       1300       1310       1320 
DTAIGIKSTG ELDVSLSDVY DFTVKQKGKE IKSFKEPVQL SLRMFDIEEA HNPAIYHVDR 

      1330       1340       1350       1360       1370       1380 
KKKAFTKTGH GSVDDDMVTG YTNHFSEYTI LNSGSNNKPP AFPSDQPTGG DDGNHGGGSD 

      1390       1400       1410       1420       1430       1440 
KPGGKQPTDG NGGNDTPPGT QPTNGSGGNG SGGSGTDGPA GGLLPDTATS MYSILLAGFL 

      1450       1460 
ISALGTAMYL HQRRKQNRAN QA 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and sequencing of a 40.6 kb segment in the 73 degrees-76 degrees region of the Bacillus subtilis chromosome containing genes for trehalose metabolism and acetoin utilization."
Yamamoto H., Uchiyama S., Sekiguchi J.
Microbiology 142:3057-3065(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168 / AC327.
[2]"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. expand/collapse author list , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 168.
[3]"Purification and characterization of yfkN, a trifunctional nucleotide phosphoesterase secreted by Bacillus subtilis."
Chambert R., Pereira Y., Petit-Glatron M.-F.
J. Biochem. 134:655-660(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 36-43 AND 955-960, FUNCTION AS A TRIFUNCTIONAL NUCLEOTIDE PHOSPHOESTERASE, CATALYTIC ACTIVITY, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY, DOMAIN N-TERMINAL, SUBCELLULAR LOCATION.
Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
[4]"Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis."
Allenby N.E.E., O'Connor N., Pragai Z., Ward A.C., Wipat A., Harwood C.R.
J. Bacteriol. 187:8063-8080(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION BY PHOSPHATE STARVATION.
Strain: 168.
[5]"Crystal structure of calcineurin-like phosphoesterase from Bacillus subtilis."
Midwest center for structural genomics (MCSG)
Submitted (APR-2009) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 37-374 IN COMPLEX WITH DIVALENT METAL CATIONS.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D83967 Genomic DNA. Translation: BAA23404.1.
AL009126 Genomic DNA. Translation: CAB12613.1.
PIRA69809.
RefSeqNP_388665.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3GVEX-ray1.25A/B37-374[»]
ProteinModelPortalO34313.
SMRO34313. Positions 41-613, 667-1180.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActO34313. 1 interaction.
STRING224308.BSU07840.

Proteomic databases

PaxDbO34313.

Protocols and materials databases

DNASU936131.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB12613; CAB12613; BSU07840.
GeneID936131.
KEGGbsu:BSU07840.
PATRIC18973216. VBIBacSub10457_0822.

Organism-specific databases

GenoListBSU07840.

Phylogenomic databases

eggNOGCOG0737.
HOGENOMHOG000008801.
KOK01119.
K08693.
OMADAQKWYA.
OrthoDBEOG696BW0.
ProtClustDBPRK09419.

Enzyme and pathway databases

BioCycBSUB:BSU07840-MONOMER.

Family and domain databases

Gene3D3.90.780.10. 2 hits.
InterProIPR008334. 5'-Nucleotdase_C.
IPR006146. 5'-Nucleotdase_CS.
IPR006179. 5_nucleotidase/apyrase.
IPR004843. Calcineurin-like_PHP_apaH.
IPR019931. LPXTG_anchor.
[Graphical view]
PANTHERPTHR11575. PTHR11575. 1 hit.
PfamPF02872. 5_nucleotid_C. 2 hits.
PF00149. Metallophos. 2 hits.
[Graphical view]
PRINTSPR01607. APYRASEFAMLY.
SUPFAMSSF55816. SSF55816. 2 hits.
PROSITEPS00785. 5_NUCLEOTIDASE_1. 2 hits.
PS00786. 5_NUCLEOTIDASE_2. 1 hit.
PS50847. GRAM_POS_ANCHORING. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO34313.

Entry information

Entry nameNTPES_BACSU
AccessionPrimary (citable) accession number: O34313
Secondary accession number(s): Q79EX6
Entry history
Integrated into UniProtKB/Swiss-Prot: January 19, 2010
Last sequence update: January 1, 1998
Last modified: April 16, 2014
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList