Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Peptide deformylase

Gene

def

Organism
Prochlorococcus marinus (strain MIT 9312)
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 bindingi121 – 1211IronUniRule annotation
Metal bindingi163 – 1631IronUniRule annotation
Active sitei164 – 1641UniRule annotation
Metal bindingi167 – 1671IronUniRule 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

BioCyciPMAR74546:GHRG-72-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:PMT9312_0070
OrganismiProchlorococcus marinus (strain MIT 9312)
Taxonomic identifieri74546 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaProchloralesProchlorococcaceaeProchlorococcus
ProteomesiUP000002715: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 201201Peptide deformylasePRO_0000301078Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi74546.PMT9312_0070.

Structurei

3D structure databases

ProteinModelPortaliQ31DB4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
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.

Q31DB4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MANHFSQLAK KSKTNGNSEK IAKEQTGKPS LEIYKLGDDV LRQNSKRITK
60 70 80 90 100
VDESIRKLTR EMIQSMYAAK GIGLAAPQIG INKELLVIDV NFEDSAAEPL
110 120 130 140 150
ILINPEITDY GTTLNSYEEG CLSIPGVYLN VVRPSTIKLK FRDEMGRPRK
160 170 180 190 200
MKADGLLARC IQHEMDHLNG ILFVDRVTSK DDLKKELIKE GFHEKDVISI

T
Length:201
Mass (Da):22,588
Last modified:December 6, 2005 - v1
Checksum:iBB0627C45E8A7F8E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000111 Genomic DNA. Translation: ABB49131.1.
RefSeqiWP_011375634.1. NC_007577.1.
YP_396567.1. NC_007577.1.

Genome annotation databases

EnsemblBacteriaiABB49131; ABB49131; PMT9312_0070.
GeneIDi3764853.
KEGGipmi:PMT9312_0070.
PATRICi23003750. VBIProMar70153_0071.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000111 Genomic DNA. Translation: ABB49131.1.
RefSeqiWP_011375634.1. NC_007577.1.
YP_396567.1. NC_007577.1.

3D structure databases

ProteinModelPortaliQ31DB4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi74546.PMT9312_0070.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB49131; ABB49131; PMT9312_0070.
GeneIDi3764853.
KEGGipmi:PMT9312_0070.
PATRICi23003750. VBIProMar70153_0071.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciPMAR74546:GHRG-72-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. "Complete sequence of Prochlorococcus marinus str. MIT 9312."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Thiel J., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A., Richardson P.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MIT 9312.

Entry informationi

Entry nameiDEF_PROM9
AccessioniPrimary (citable) accession number: Q31DB4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: December 6, 2005
Last modified: February 4, 2015
This is version 60 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. 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.