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Protein

Formamidase

Gene

amiF

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide. Probably involved in the nitrogen metabolism of H.pylori.1 Publication

Catalytic activityi

Formamide + H2O = formate + NH3.1 Publication

Enzyme regulationi

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

pH dependencei

Optimum pH is 6.1 Publication

Temperature dependencei

Optimum temperature is 45 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei60 – 601Proton acceptorBy similarity
Active sitei133 – 1331Proton donorBy similarity
Active sitei166 – 1661NucleophileBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BRENDAi3.5.1.49. 2604.

Names & Taxonomyi

Protein namesi
Recommended name:
Formamidase (EC:3.5.1.49)
Alternative name(s):
Formamide amidohydrolase
Gene namesi
Name:amiF
Ordered Locus Names:HP_1238
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000429 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi166 – 1661C → S or A: Loss of activity. 1 Publication
Mutagenesisi168 – 1681D → A: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 334334FormamidasePRO_0000204065Add
BLAST

Proteomic databases

PaxDbiO25836.
PRIDEiO25836.

Expressioni

Inductioni

Contrary to the other amidase AmiE, expression of amiF is not repressed by iron.1 Publication

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

IntActiO25836. 3 interactions.
MINTiMINT-164907.
STRINGi85962.HP1238.

Structurei

Secondary structure

1
334
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 196Combined sources
Helixi29 – 4921Combined sources
Beta strandi53 – 575Combined sources
Turni60 – 645Combined sources
Turni68 – 725Combined sources
Helixi74 – 763Combined sources
Beta strandi80 – 823Combined sources
Helixi83 – 9513Combined sources
Beta strandi98 – 1058Combined sources
Beta strandi115 – 1217Combined sources
Beta strandi127 – 1326Combined sources
Turni138 – 1403Combined sources
Helixi156 – 1583Combined sources
Beta strandi160 – 1656Combined sources
Helixi166 – 1705Combined sources
Helixi172 – 1809Combined sources
Beta strandi184 – 1929Combined sources
Beta strandi194 – 1963Combined sources
Helixi197 – 21115Combined sources
Beta strandi214 – 2196Combined sources
Beta strandi221 – 2266Combined sources
Beta strandi232 – 2365Combined sources
Beta strandi242 – 2454Combined sources
Beta strandi253 – 2586Combined sources
Helixi260 – 26910Combined sources
Helixi275 – 2784Combined sources
Turni284 – 2885Combined sources
Helixi297 – 3037Combined sources
Helixi312 – 3143Combined sources
Beta strandi318 – 3203Combined sources
Helixi321 – 3233Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliO25836.
SMRiO25836. Positions 13-334.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO25836.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 287274CN hydrolaseAdd
BLAST

Sequence similaritiesi

Contains 1 CN hydrolase domain.Curated

Phylogenomic databases

eggNOGiENOG4105DCY. Bacteria.
COG0388. LUCA.
KOiK01455.
OMAiVENNIYQ.
OrthoDBiEOG6C5RKP.

Family and domain databases

Gene3Di3.60.110.10. 1 hit.
HAMAPiMF_01243. Formamidase.
InterProiIPR003010. C-N_Hydrolase.
IPR022843. Formamidase.
[Graphical view]
PfamiPF00795. CN_hydrolase. 1 hit.
[Graphical view]
SUPFAMiSSF56317. SSF56317. 1 hit.
PROSITEiPS50263. CN_HYDROLASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O25836-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGSIGSMGKP IEGFLVAAIQ FPVPIVNSRK DIDHNIESII RTLHATKAGY
60 70 80 90 100
PGVELIIFPE YSTQGLNTAK WLSEEFLLDV PGKETELYAK ACKEAKVYGV
110 120 130 140 150
FSIMERNPDS NKNPYNTAII IDPQGEIILK YRKLFPWNPI EPWYPGDLGM
160 170 180 190 200
PVCEGPGGSK LAVCICHDGM IPELAREAAY KGCNVYIRIS GYSTQVNDQW
210 220 230 240 250
ILTNRSNAWH NLMYTVSVNL AGYDNVFYYF GEGQICNFDG TTLVQGHRNP
260 270 280 290 300
WEIVTGEIYP KMADNARLSW GLENNIYNLG HRGYVAKPGG EHDAGLTYIK
310 320 330
DLAAGKYKLP WEDHMKIKDG SIYGYPTTGG RFGK
Length:334
Mass (Da):37,291
Last modified:January 1, 1998 - v1
Checksum:iB2845E0902A40420
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD08283.1.
PIRiF64674.
RefSeqiNP_208030.1. NC_000915.1.
WP_000534771.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD08283; AAD08283; HP_1238.
GeneIDi900367.
KEGGiheo:C694_06390.
hpy:HP1238.
PATRICi20593847. VBIHelPyl33062_1294.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD08283.1.
PIRiF64674.
RefSeqiNP_208030.1. NC_000915.1.
WP_000534771.1. NC_018939.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliO25836.
SMRiO25836. Positions 13-334.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO25836. 3 interactions.
MINTiMINT-164907.
STRINGi85962.HP1238.

Proteomic databases

PaxDbiO25836.
PRIDEiO25836.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD08283; AAD08283; HP_1238.
GeneIDi900367.
KEGGiheo:C694_06390.
hpy:HP1238.
PATRICi20593847. VBIHelPyl33062_1294.

Phylogenomic databases

eggNOGiENOG4105DCY. Bacteria.
COG0388. LUCA.
KOiK01455.
OMAiVENNIYQ.
OrthoDBiEOG6C5RKP.

Enzyme and pathway databases

BRENDAi3.5.1.49. 2604.

Miscellaneous databases

EvolutionaryTraceiO25836.

Family and domain databases

Gene3Di3.60.110.10. 1 hit.
HAMAPiMF_01243. Formamidase.
InterProiIPR003010. C-N_Hydrolase.
IPR022843. Formamidase.
[Graphical view]
PfamiPF00795. CN_hydrolase. 1 hit.
[Graphical view]
SUPFAMiSSF56317. SSF56317. 1 hit.
PROSITEiPS50263. CN_HYDROLASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. 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.

Entry informationi

Entry nameiAMIF_HELPY
AccessioniPrimary (citable) accession number: O25836
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2003
Last sequence update: January 1, 1998
Last modified: November 11, 2015
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.1 Publication
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.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  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.