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Protein

Peptide deformylase

Gene

def

Organism
Hamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT)
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 bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule 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

BioCyciHDEF572265:GJAB-1736-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:HDEF_1720
OrganismiHamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT)
Taxonomic identifieri572265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeaphid secondary symbiontsCandidatus Hamiltonella
ProteomesiUP000002334 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 171171Peptide deformylasePRO_1000203604Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi572265.HDEF_1720.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiLEIIHYP.
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.

C4K6Y0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSILQILHFP DDRLRKIASP VKKMDDQIRQ IADDMLETMY QAEGIGLAAT
60 70 80 90 100
QVNIHQRIIV IDVSEDRHQP LILINPELLE KSGETGIEEG CLSIPGEKAF
110 120 130 140 150
IPRAKEITIQ ALNREGRSFR LSADDLLAIC IQHEMDHLIG KLFVDYLSPF
160 170
KRQRIQKKME KLQKINEKKD K
Length:171
Mass (Da):19,668
Last modified:July 6, 2009 - v1
Checksum:i2895AAEC85926923
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001277 Genomic DNA. Translation: ACQ68323.1.
RefSeqiYP_002924471.1. NC_012751.1.

Genome annotation databases

EnsemblBacteriaiACQ68323; ACQ68323; HDEF_1720.
GeneIDi7951317.
KEGGihde:HDEF_1720.
PATRICi31974899. VBICanHam112931_1710.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001277 Genomic DNA. Translation: ACQ68323.1.
RefSeqiYP_002924471.1. NC_012751.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi572265.HDEF_1720.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACQ68323; ACQ68323; HDEF_1720.
GeneIDi7951317.
KEGGihde:HDEF_1720.
PATRICi31974899. VBICanHam112931_1710.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciHDEF572265:GJAB-1736-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. "Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors."
    Degnan P.H., Yu Y., Sisneros N., Wing R.A., Moran N.A.
    Proc. Natl. Acad. Sci. U.S.A. 106:9063-9068(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 5AT.

Entry informationi

Entry nameiDEF_HAMD5
AccessioniPrimary (citable) accession number: C4K6Y0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 21, 2009
Last sequence update: July 6, 2009
Last modified: February 3, 2015
This is version 37 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.