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Protein

Peptide deformylase 1

Gene

def1

Organism
Nostoc sp. (strain PCC 7120 / UTEX 2576)
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 bindingi107 – 1071IronUniRule annotation
Metal bindingi149 – 1491IronUniRule annotation
Active sitei150 – 1501UniRule annotation
Metal bindingi153 – 1531IronUniRule annotation

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 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:alr3079
OrganismiNostoc sp. (strain PCC 7120 / UTEX 2576)
Taxonomic identifieri103690 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaNostocalesNostocaceaeNostoc
ProteomesiUP000002483 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 187187Peptide deformylase 1PRO_0000082730Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi103690.alr3079.

Structurei

3D structure databases

ProteinModelPortaliQ8YSK6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
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.

Q8YSK6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPSEIAVEKK KLKNPPLQLH YLGDRVLRQP AKRITKVDDE TRQLIRDMLQ
60 70 80 90 100
TMYSSDGIGL AAPQVGINKQ LIVIDCEPDN PANPPLILIN PTIKQVSREI
110 120 130 140 150
CSAQEGCLSI PGVYMDVKRP EVVEVAYKDE NGRPQTLKAT DLLGRCIQHE
160 170 180
MDHLNGVVFV DRVDNSLTLA QELSKNGFSY QAVKPVA
Length:187
Mass (Da):20,827
Last modified:March 1, 2002 - v1
Checksum:iFB06469799C55CA4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000019 Genomic DNA. Translation: BAB74778.1.
PIRiAH2190.
RefSeqiNP_487119.1. NC_003272.1.
WP_010997230.1. NC_003272.1.

Genome annotation databases

EnsemblBacteriaiBAB74778; BAB74778; BAB74778.
KEGGiana:alr3079.
PATRICi22776496. VBINosSp37423_3708.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000019 Genomic DNA. Translation: BAB74778.1.
PIRiAH2190.
RefSeqiNP_487119.1. NC_003272.1.
WP_010997230.1. NC_003272.1.

3D structure databases

ProteinModelPortaliQ8YSK6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi103690.alr3079.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB74778; BAB74778; BAB74778.
KEGGiana:alr3079.
PATRICi22776496. VBINosSp37423_3708.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
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.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 7120 / UTEX 2576.

Entry informationi

Entry nameiDEF1_NOSS1
AccessioniPrimary (citable) accession number: Q8YSK6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: March 1, 2002
Last modified: April 29, 2015
This is version 73 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.