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Protein

Peptide deformylase

Gene

def

Organism
Natranaerobius thermophilus (strain ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF)
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 bindingi90 – 901IronUniRule annotation
Metal bindingi132 – 1321IronUniRule annotation
Active sitei133 – 1331UniRule annotation
Metal bindingi136 – 1361IronUniRule annotation

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciNTHE457570:GHRL-1369-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:Nther_1333
OrganismiNatranaerobius thermophilus (strain ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF)
Taxonomic identifieri457570 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaNatranaerobialesNatranaerobiaceaeNatranaerobius
ProteomesiUP000001683: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 156156Peptide deformylasePRO_1000097326Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi457570.Nther_1333.

Structurei

3D structure databases

ProteinModelPortaliB2A2K1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
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.

B2A2K1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIKKIRTND DPVLKRKAKK VTNIDDRLER LLTNMLDTMY EAEGIGLAAP
60 70 80 90 100
QIGISKRVIV VDIGEDEIYQ LINPEIVDTS DEQEKALEGC LSYPGLQGRV
110 120 130 140 150
TRPVKVTVKA LNPQEEEMII EAEGLLARAL QHEIDHLDGI TFIDRAEEVF

REEESH
Length:156
Mass (Da):17,621
Last modified:May 20, 2008 - v1
Checksum:iA682723B9CA10EEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001034 Genomic DNA. Translation: ACB84916.1.
RefSeqiYP_001917504.1. NC_010718.1.

Genome annotation databases

EnsemblBacteriaiACB84916; ACB84916; Nther_1333.
GeneIDi6314443.
KEGGinth:Nther_1333.
PATRICi22671332. VBINatThe92436_1368.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001034 Genomic DNA. Translation: ACB84916.1.
RefSeqiYP_001917504.1. NC_010718.1.

3D structure databases

ProteinModelPortaliB2A2K1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi457570.Nther_1333.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB84916; ACB84916; Nther_1333.
GeneIDi6314443.
KEGGinth:Nther_1333.
PATRICi22671332. VBINatThe92436_1368.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciNTHE457570:GHRL-1369-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. "Complete sequence of chromosome of Natranaerobius thermophilus JW/NM-WN-LF."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.
    , Kyrpides N., Lykidis A., Mesbah N.M., Wiegel J.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF.

Entry informationi

Entry nameiDEF_NATTJ
AccessioniPrimary (citable) accession number: B2A2K1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: February 4, 2015
This is version 48 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.