Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

O25836 (AMIF_HELPY) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 83. 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:
Formamidase

EC=3.5.1.49
Alternative name(s):
Formamide amidohydrolase
Gene names
Name:amiF
Ordered Locus Names:HP_1238
OrganismHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]
Taxonomic identifier85962 [NCBI]
Taxonomic lineageBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter

Protein attributes

Sequence length334 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide. Probably involved in the nitrogen metabolism of H.pylori. Ref.2

Catalytic activity

Formamide + H2O = formate + NH3. Ref.2

Enzyme regulation

Inhibited by iodoacetate. Appears to be regulated by the fur protein, but this effect is not mediated at the transcriptional level. Ref.2 Ref.3

Subunit structure

Homotetramer. Ref.2

Induction

Contrary to the other amidase AmiE, expression of amiF is not repressed by iron. Ref.2 Ref.3

Miscellaneous

Asp-168 is probably not involved in the catalytic mechanism, but is probably involved instead in maintenance of the structural integrity of the amidase (Ref.2).

Expression of the amiF gene is stimulated in a mutant deficient in arginase activity, suggesting that production of this enzyme is regulated to maintain intracellular nitrogen balance in H.pylori.

Sequence similarities

Belongs to the carbon-nitrogen hydrolase superfamily. Aliphatic amidase family.

Contains 1 CN hydrolase domain.

Biophysicochemical properties

pH dependence:

Optimum pH is 6. Ref.2

Temperature dependence:

Optimum temperature is 45 degrees Celsius.

Ontologies

Keywords
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processnitrogen compound metabolic process

Inferred from electronic annotation. Source: InterPro

   Molecular_functionformamidase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 334334Formamidase HAMAP-Rule MF_01243
PRO_0000204065

Regions

Domain14 – 287274CN hydrolase

Sites

Active site601Proton acceptor Potential
Active site1331 Potential
Active site1661Nucleophile Probable

Experimental info

Mutagenesis1661C → S or A: Loss of activity. Ref.2
Mutagenesis1681D → A: Loss of activity. Ref.2

Secondary structure

........................................................... 334
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O25836 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: B2845E0902A40420

FASTA33437,291
        10         20         30         40         50         60 
MGSIGSMGKP IEGFLVAAIQ FPVPIVNSRK DIDHNIESII RTLHATKAGY PGVELIIFPE 

        70         80         90        100        110        120 
YSTQGLNTAK WLSEEFLLDV PGKETELYAK ACKEAKVYGV FSIMERNPDS NKNPYNTAII 

       130        140        150        160        170        180 
IDPQGEIILK YRKLFPWNPI EPWYPGDLGM PVCEGPGGSK LAVCICHDGM IPELAREAAY 

       190        200        210        220        230        240 
KGCNVYIRIS GYSTQVNDQW ILTNRSNAWH NLMYTVSVNL AGYDNVFYYF GEGQICNFDG 

       250        260        270        280        290        300 
TTLVQGHRNP WEIVTGEIYP KMADNARLSW GLENNIYNLG HRGYVAKPGG EHDAGLTYIK 

       310        320        330 
DLAAGKYKLP WEDHMKIKDG SIYGYPTTGG RFGK 

« Hide

References

« Hide 'large scale' references
[1]"The complete genome sequence of the gastric pathogen Helicobacter pylori."
Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. expand/collapse author list , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.
Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700392 / 26695.
[2]"The AmiE aliphatic amidase and AmiF formamidase of Helicobacter pylori: natural evolution of two enzyme paralogues."
Skouloubris S., Labigne A., De Reuse H.
Mol. Microbiol. 40:596-609(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, MUTAGENESIS OF CYS-166 AND ASP-168.
[3]"Differential regulation of amidase- and formamidase-mediated ammonia production by the Helicobacter pylori fur repressor."
van Vliet A.H.M., Stoof J., Poppelaars S.W., Bereswill S., Homuth G., Kist M., Kuipers E.J., Kusters J.G.
J. Biol. Chem. 278:9052-9057(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION, INDUCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000511 Genomic DNA. Translation: AAD08283.1.
PIRF64674.
RefSeqNP_208030.1. NC_000915.1.
YP_006935156.1. NC_018939.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2DYUX-ray1.75A/B1-334[»]
2DYVX-ray2.00A/B1-334[»]
2E2KX-ray2.50A/B/C/D/E/F1-334[»]
2E2LX-ray2.29A/B/C/D/E/F1-334[»]
ProteinModelPortalO25836.
SMRO25836. Positions 13-334.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActO25836. 3 interactions.
MINTMINT-164907.
STRING85962.HP1238.

Proteomic databases

PRIDEO25836.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAD08283; AAD08283; HP_1238.
GeneID13870443.
900367.
KEGGheo:C694_06390.
hpy:HP1238.
PATRIC20593847. VBIHelPyl33062_1294.

Phylogenomic databases

eggNOGCOG0388.
KOK01455.
OMAIICHDGM.
OrthoDBEOG6C5RKP.
ProtClustDBPRK13287.

Family and domain databases

Gene3D3.60.110.10. 1 hit.
HAMAPMF_01243. Formamidase.
InterProIPR003010. C-N_Hydrolase.
IPR022843. Formamidase.
[Graphical view]
PfamPF00795. CN_hydrolase. 1 hit.
[Graphical view]
SUPFAMSSF56317. SSF56317. 1 hit.
PROSITEPS50263. CN_HYDROLASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO25836.

Entry information

Entry nameAMIF_HELPY
AccessionPrimary (citable) accession number: O25836
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2003
Last sequence update: January 1, 1998
Last modified: March 19, 2014
This is version 83 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

Helicobacter pylori

Helicobacter pylori (strain 26695): entries and gene names