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Protein

Peptide deformylase

Gene

def

Organism
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Status
Reviewed-Annotation score: Annotation score: 3 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 bindingi94 – 941IronUniRule annotation
Metal bindingi136 – 1361IronUniRule annotation
Active sitei137 – 1371UniRule annotation
Metal bindingi140 – 1401IronUniRule 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

BioCyciBMEL224914:GCJ0-2381-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:BMEII0264
OrganismiBrucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Taxonomic identifieri224914 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeBrucella
ProteomesiUP000000419 Componenti: Chromosome II

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 175175Peptide deformylasePRO_0000082752Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224914.BAWG_2294.

Structurei

3D structure databases

ProteinModelPortaliP63913.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
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.

P63913-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVKPLIILP DPVLRQVSKP VERFDDQLRK FASDMFDTMY DAPGIGLAAI
60 70 80 90 100
QVGEPIRMLV IDLAKEGEPK APHIFVNPTI VQSSDKRSTY EEGCLSIPDY
110 120 130 140 150
YAEVERPATV KVNYFDADGK PQSMEADGLM ATCLQHEIDH LNGVLFIDHI
160 170
SKLKRDMVIK KFKKLASQRA SKKVL
Length:175
Mass (Da):19,660
Last modified:October 11, 2004 - v1
Checksum:i873A6ABCF3EFFCE2
GO

Sequence cautioni

The sequence AAL53505.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008918 Genomic DNA. Translation: AAL53505.1. Different initiation.
PIRiAF3542.
RefSeqiNP_541241.1. NC_003318.1.
WP_002965616.1. NZ_GG703779.1.

Genome annotation databases

EnsemblBacteriaiAAL53505; AAL53505; BMEII0264.
GeneIDi3828148.
KEGGibme:BMEII0264.
PATRICi17855164. VBIBruMel92729_2553.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008918 Genomic DNA. Translation: AAL53505.1. Different initiation.
PIRiAF3542.
RefSeqiNP_541241.1. NC_003318.1.
WP_002965616.1. NZ_GG703779.1.

3D structure databases

ProteinModelPortaliP63913.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224914.BAWG_2294.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL53505; AAL53505; BMEII0264.
GeneIDi3828148.
KEGGibme:BMEII0264.
PATRICi17855164. VBIBruMel92729_2553.

Phylogenomic databases

HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciBMEL224914:GCJ0-2381-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: 16M / ATCC 23456 / NCTC 10094.

Entry informationi

Entry nameiDEF_BRUME
AccessioniPrimary (citable) accession number: P63913
Secondary accession number(s): Q8YDB4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: June 24, 2015
This is version 63 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

Documents

  1. Brucella melitensis
    Brucella melitensis (strain 16M): entries and gene names
  2. 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.