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Protein

Peptide deformylase

Gene

def

Organism
Bradyrhizobium sp. (strain ORS278)
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 bindingi98 – 981IronUniRule annotation
Metal bindingi140 – 1401IronUniRule annotation
Active sitei141 – 1411UniRule annotation
Metal bindingi144 – 1441IronUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciBSP114615:GJN5-731-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:BRADO0770
OrganismiBradyrhizobium sp. (strain ORS278)
Taxonomic identifieri114615 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000001994 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 175175Peptide deformylasePRO_0000301013Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi114615.BRADO0770.

Structurei

3D structure databases

ProteinModelPortaliA4YLB9.
SMRiA4YLB9. Positions 2-172.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
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.

A4YLB9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLREIIILP DRQLRLVSKP VEKVTPEIRQ LVDDMFQTMY DAPGIGLAAI
60 70 80 90 100
QVAQPLRVIT MDLAKPDSGG ETKREPRVFI NPEIIAKSDE LSVYEEGCLS
110 120 130 140 150
IPEYYEEVER PARVRVRFTD LDGVVREEDA EGLYATCIQH EIDHLNGVLF
160 170
IDYLSKLKRD RVMKKFTKAA KRAGE
Length:175
Mass (Da):19,976
Last modified:May 29, 2007 - v1
Checksum:i49B0C8291E41D5C7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU234118 Genomic DNA. Translation: CAL74695.1.
RefSeqiWP_011923950.1. NC_009445.1.

Genome annotation databases

EnsemblBacteriaiCAL74695; CAL74695; BRADO0770.
KEGGibra:BRADO0770.
PATRICi21217803. VBIBraSp122330_0731.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU234118 Genomic DNA. Translation: CAL74695.1.
RefSeqiWP_011923950.1. NC_009445.1.

3D structure databases

ProteinModelPortaliA4YLB9.
SMRiA4YLB9. Positions 2-172.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi114615.BRADO0770.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL74695; CAL74695; BRADO0770.
KEGGibra:BRADO0770.
PATRICi21217803. VBIBraSp122330_0731.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciBSP114615:GJN5-731-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ORS278.

Entry informationi

Entry nameiDEF_BRASO
AccessioniPrimary (citable) accession number: A4YLB9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: May 29, 2007
Last modified: July 22, 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.