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Protein

Peptide deformylase

Gene

def

Organism
Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
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 bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule annotation

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciNGON242231:GI2G-1775-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:NGO1871
OrganismiNeisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
Taxonomic identifieri242231 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNeisserialesNeisseriaceaeNeisseria
ProteomesiUP000000535: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 167167Peptide deformylasePRO_0000301066Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi242231.NGO1871.

Structurei

3D structure databases

ProteinModelPortaliQ5F5P6.
SMRiQ5F5P6. Positions 2-165.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDTMLEMD.
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.

Q5F5P6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLNILQYP DERLHTVAKP VEQVDERIRK LVADMFETMY ESRGIGLAAT
60 70 80 90 100
QVDVHERVVV MDLTEDRSEP RVFINPVIVE KDGETTYEEG CLSVPGIYDA
110 120 130 140 150
VTRAERVKVE ALNEKGEKFT LEADGLLAIC VQHELDHLMG IVFVERLSQL
160
KQGRIKTKLK KRQKHTI
Length:167
Mass (Da):19,071
Last modified:March 15, 2005 - v1
Checksum:i9BB11DB3BAC71BD3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004969 Genomic DNA. Translation: AAW90491.1.
RefSeqiYP_208903.1. NC_002946.2.

Genome annotation databases

EnsemblBacteriaiAAW90491; AAW90491; NGO1871.
GeneIDi3282344.
KEGGingo:NGO1871.
PATRICi20337436. VBINeiGon24812_2249.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004969 Genomic DNA. Translation: AAW90491.1.
RefSeqiYP_208903.1. NC_002946.2.

3D structure databases

ProteinModelPortaliQ5F5P6.
SMRiQ5F5P6. Positions 2-165.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi242231.NGO1871.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAW90491; AAW90491; NGO1871.
GeneIDi3282344.
KEGGingo:NGO1871.
PATRICi20337436. VBINeiGon24812_2249.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDTMLEMD.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciNGON242231:GI2G-1775-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. "The complete genome sequence of Neisseria gonorrhoeae."
    Lewis L.A., Gillaspy A.F., McLaughlin R.E., Gipson M., Ducey T.F., Ownbey T., Hartman K., Nydick C., Carson M.B., Vaughn J., Thomson C., Song L., Lin S., Yuan X., Najar F., Zhan M., Ren Q., Zhu H.
    , Qi S., Kenton S.M., Lai H., White J.D., Clifton S., Roe B.A., Dyer D.W.
    Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700825 / FA 1090.

Entry informationi

Entry nameiDEF_NEIG1
AccessioniPrimary (citable) accession number: Q5F5P6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: March 15, 2005
Last modified: January 7, 2015
This is version 59 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.