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Protein

Peptide deformylase

Gene

def

Organism
Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
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)DescriptionActionsGraphical viewLength
Metal bindingi91IronBy similarity1
Metal bindingi133IronBy similarity1
Active sitei134By similarity1
Metal bindingi137IronBy similarity1

GO - Molecular functioni

GO - Biological processi

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 (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Ordered Locus Names:BU496
OrganismiBuchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
Taxonomic identifieri107806 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesErwiniaceaeBuchnera
Proteomesi
  • UP000001806 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000827541 – 173Peptide deformylaseAdd BLAST173

Interactioni

Protein-protein interaction databases

STRINGi107806.BU496.

Structurei

3D structure databases

ProteinModelPortaliP57563.
SMRiP57563.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
KOiK01462.
OMAiVCIQHEI.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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.

P57563-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLLKILYYP DIRLRILAKP VKEINKKIQK IANDMIDTMY QEEGIGLAAT
60 70 80 90 100
QVNIPLQIIV VNTMEQKKNN LVLINPKIIK KEGDISIEEG CLSIPEYQAS
110 120 130 140 150
IPRSNYIQVQ AVNLDGEKIE IEAKSILSIC IQHEIDHLKG KLFIDYLSKF
160 170
KRERIQKKFE KINKKNKKFS IKE
Length:173
Mass (Da):20,038
Last modified:December 1, 2000 - v1
Checksum:iBAF78C26E56BED31
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000003 Genomic DNA. Translation: BAB13189.1.
RefSeqiNP_240303.1. NC_002528.1.
WP_009874447.1. NC_002528.1.

Genome annotation databases

EnsemblBacteriaiBAB13189; BAB13189; BAB13189.
GeneIDi1109839.
KEGGibuc:BU496.
PATRICi21244534. VBIBucAph127364_0501.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000003 Genomic DNA. Translation: BAB13189.1.
RefSeqiNP_240303.1. NC_002528.1.
WP_009874447.1. NC_002528.1.

3D structure databases

ProteinModelPortaliP57563.
SMRiP57563.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi107806.BU496.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB13189; BAB13189; BAB13189.
GeneIDi1109839.
KEGGibuc:BU496.
PATRICi21244534. VBIBucAph127364_0501.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
KOiK01462.
OMAiVCIQHEI.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

Entry informationi

Entry nameiDEF_BUCAI
AccessioniPrimary (citable) accession number: P57563
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: November 2, 2016
This is version 90 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. Buchnera aphidicola (subsp. Acyrthosiphon pisum)
    Buchnera aphidicola (subsp. Acyrthosiphon pisum): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.