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Protein

Peptide deformylase

Gene

def

Organism
Nautilia profundicola (strain ATCC BAA-1463 / DSM 18972 / AmH)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.UniRule annotation

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi96 – 961IronUniRule annotation
Metal bindingi138 – 1381IronUniRule annotation
Active sitei139 – 1391UniRule annotation
Metal bindingi142 – 1421IronUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciNPRO598659:GH7N-1721-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:NAMH_1729
OrganismiNautilia profundicola (strain ATCC BAA-1463 / DSM 18972 / AmH)
Taxonomic identifieri598659 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaNautilialesNautiliaceaeNautilia
ProteomesiUP000000448 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 174174Peptide deformylasePRO_1000200742Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi598659.NAMH_1729.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

B9L6X1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVLDIVTYP NKVLKQISKP VERFDKDLHK LLDDMYETMI KNNGVGLAAI
60 70 80 90 100
QVAVPIRALL IDIGDEEGKQ SKDTLIEVIN PEFLTWDGTQ KDTEGCLSVP
110 120 130 140 150
DYFDEVERYK NVKVKFFDRF GKEHVMEAEG LLSVAFQHET DHLDGHLFVE
160 170
RLDYIKRKKF EKEWKKLLKQ KRKK
Length:174
Mass (Da):20,341
Last modified:March 24, 2009 - v1
Checksum:i04087CD59657E845
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001279 Genomic DNA. Translation: ACM93397.1.
RefSeqiWP_015902449.1. NC_012115.1.
YP_002608109.1. NC_012115.1.

Genome annotation databases

EnsemblBacteriaiACM93397; ACM93397; NAMH_1729.
KEGGinam:NAMH_1729.
PATRICi22678151. VBINauPro131435_1671.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001279 Genomic DNA. Translation: ACM93397.1.
RefSeqiWP_015902449.1. NC_012115.1.
YP_002608109.1. NC_012115.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi598659.NAMH_1729.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACM93397; ACM93397; NAMH_1729.
KEGGinam:NAMH_1729.
PATRICi22678151. VBINauPro131435_1671.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciNPRO598659:GH7N-1721-MONOMER.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola."
    Campbell B.J., Smith J.L., Hanson T.E., Klotz M.G., Stein L.Y., Lee C.K., Wu D., Robinson J.M., Khouri H.M., Eisen J.A., Cary S.C.
    PLoS Genet. 5:E1000362-E1000362(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-1463 / DSM 18972 / AmH.

Entry informationi

Entry nameiDEF_NAUPA
AccessioniPrimary (citable) accession number: B9L6X1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: May 27, 2015
This is version 45 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.