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Protein

Peptide deformylase

Gene

def

Organism
Phenylobacterium zucineum (strain HLK1)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi94IronUniRule annotation1
Metal bindingi136IronUniRule annotation1
Active sitei137UniRule annotation1
Metal bindingi140IronUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding

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:PHZ_c0373
OrganismiPhenylobacterium zucineum (strain HLK1)
Taxonomic identifieri450851 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaePhenylobacterium
Proteomesi
  • UP000001868 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000973311 – 169Peptide deformylaseAdd BLAST169

Proteomic databases

PRIDEiB4RDT8

Interactioni

Protein-protein interaction databases

STRINGi450851.PHZ_c0373

Structurei

3D structure databases

SMRiB4RDT8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
HOGENOMiHOG000243509
KOiK01462
OMAiVCIQHEI
OrthoDBiPOG091H02B0

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
PIRSFiPIRSF004749 Pep_def, 1 hit
PRINTSiPR01576 PDEFORMYLASE
SUPFAMiSSF56420 SSF56420, 1 hit
TIGRFAMsiTIGR00079 pept_deformyl, 1 hit

Sequencei

Sequence statusi: Complete.

B4RDT8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIREILVVP HPALKQVSQP VEKVDDELRA LMDDMLETMY AAPGIGLAAI
60 70 80 90 100
QIGVPKRVIV MDLAREGEEK QPRYFVNPEI LWASDDTAPY EEGCLSVPEY
110 120 130 140 150
YDEVERPARV KLRYLNYQGE QVEEDAEGLF AVCIQHEMDH LEGVLFIDHL
160
SRLKREQAIK KVKKHAKAA
Length:169
Mass (Da):19,255
Last modified:September 23, 2008 - v1
Checksum:i1A32B4B2E9EE7FAD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000747 Genomic DNA Translation: ACG76787.1
RefSeqiWP_012520935.1, NC_011144.1

Genome annotation databases

EnsemblBacteriaiACG76787; ACG76787; PHZ_c0373
KEGGipzu:PHZ_c0373

Similar proteinsi

Entry informationi

Entry nameiDEF_PHEZH
AccessioniPrimary (citable) accession number: B4RDT8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: May 23, 2018
This is version 58 of the entry and version 1 of the sequence. See 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
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Main funding by: National Institutes of Health