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Protein

Peptide deformylase 3

Gene

def3

Organism
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
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 (By similarity).By similarity

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi120 – 1201IronBy similarity
Metal bindingi162 – 1621IronBy similarity
Active sitei163 – 1631By similarity
Metal bindingi166 – 1661IronBy similarity

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

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 3 (EC:3.5.1.88)
Short name:
PDF 3
Alternative name(s):
Polypeptide deformylase 3
Gene namesi
Name:def3
Ordered Locus Names:SCO4560
ORF Names:SCD16A.23
OrganismiStreptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
Taxonomic identifieri100226 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptomycineaeStreptomycetaceaeStreptomycesStreptomyces albidoflavus group
ProteomesiUP000001973 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 208208Peptide deformylase 3PRO_0000082854Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi100226.SCO4560.

Structurei

3D structure databases

ProteinModelPortaliQ9XAQ2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
InParanoidiQ9XAQ2.
KOiK01462.
OMAiIRFRYQD.
OrthoDBiEOG664CMF.
PhylomeDBiQ9XAQ2.

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]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9XAQ2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPSVFVQGRP TASYPPFAPE AGRGAVRRVT EVGEEVLHRP CRDVTEFGPD
60 70 80 90 100
LAALIDDMFR TMYVAEGAGL AANQVGVDLR LFVYDCPDDE GVRHVGHLVN
110 120 130 140 150
PVLDALDPAA RRLLDEGEGC LSVPGAVMAV PRPDRAVVRG LDKDGVPLLV
160 170 180 190 200
EGTGYFARCL AHETDHVNGH VYLDRLSGRE RKAALRQSAD RREEVFARRA

ANAAAFAA
Length:208
Mass (Da):22,514
Last modified:November 1, 1999 - v1
Checksum:iB72FB5E228BB844C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL939120 Genomic DNA. Translation: CAB44533.1.
PIRiT34626.
RefSeqiNP_628722.1. NC_003888.3.

Genome annotation databases

GeneIDi1100000.
KEGGisco:SCO4560.
PATRICi23738936. VBIStrCoe124346_4632.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL939120 Genomic DNA. Translation: CAB44533.1.
PIRiT34626.
RefSeqiNP_628722.1. NC_003888.3.

3D structure databases

ProteinModelPortaliQ9XAQ2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi100226.SCO4560.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1100000.
KEGGisco:SCO4560.
PATRICi23738936. VBIStrCoe124346_4632.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
InParanoidiQ9XAQ2.
KOiK01462.
OMAiIRFRYQD.
OrthoDBiEOG664CMF.
PhylomeDBiQ9XAQ2.

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]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-471 / A3(2) / M145.

Entry informationi

Entry nameiDEF3_STRCO
AccessioniPrimary (citable) accession number: Q9XAQ2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: April 1, 2015
This is version 98 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.