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Protein

Peptide deformylase 1

Gene

def1

Organism
Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)
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 bindingi99 – 991IronUniRule annotation
Metal bindingi141 – 1411IronUniRule annotation
Active sitei142 – 1421UniRule annotation
Metal bindingi145 – 1451IronUniRule 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

BioCyciXCAM190485:GIXZ-686-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
Ordered Locus Names:XCC0687
OrganismiXanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)
Taxonomic identifieri190485 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
ProteomesiUP000001010 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 171171Peptide deformylase 1PRO_0000082885Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi190485.XCC0687.

Structurei

3D structure databases

ProteinModelPortaliQ8PCN7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiHECDHLA.
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.

Q8PCN7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIREIIRMGD KRLLRVAPPV TNLGSDELHA LVADMFETMD AARGVGLAAP
60 70 80 90 100
QIAVDLQLMV FGFEASERYP EAPAVPRTAL ANVQIEPLSD EMENGWEGCL
110 120 130 140 150
SIPGLRAVIP RHRVIRYSGF APDGTPIERE AEGFHARVVQ HEYDHLVGRL
160 170
YPSRIENFDT FGFEDVLSYD L
Length:171
Mass (Da):19,106
Last modified:October 1, 2002 - v1
Checksum:i92C65439C03E1F1E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008922 Genomic DNA. Translation: AAM40003.1.
RefSeqiNP_636079.1. NC_003902.1.
WP_011035927.1. NC_003902.1.

Genome annotation databases

EnsemblBacteriaiAAM40003; AAM40003; XCC0687.
GeneIDi1001340.
KEGGixcc:XCC0687.
PATRICi24072034. VBIXanCam115730_0752.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008922 Genomic DNA. Translation: AAM40003.1.
RefSeqiNP_636079.1. NC_003902.1.
WP_011035927.1. NC_003902.1.

3D structure databases

ProteinModelPortaliQ8PCN7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi190485.XCC0687.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM40003; AAM40003; XCC0687.
GeneIDi1001340.
KEGGixcc:XCC0687.
PATRICi24072034. VBIXanCam115730_0752.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiHECDHLA.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciXCAM190485:GIXZ-686-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...

Entry informationi

Entry nameiDEF1_XANCP
AccessioniPrimary (citable) accession number: Q8PCN7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: October 1, 2002
Last modified: May 27, 2015
This is version 76 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.