Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

B4S291 (DEF_ALTMD) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 42. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptide deformylase

Short name=PDF
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:def
Ordered Locus Names:MADE_1000105
OrganismAlteromonas macleodii (strain DSM 17117 / Deep ecotype) [Complete proteome] [HAMAP]
Taxonomic identifier314275 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesAlteromonadaceaeAlteromonas

Protein attributes

Sequence length169 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 By similarity. HAMAP-Rule MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP-Rule MF_00163

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 169169Peptide deformylase HAMAP-Rule MF_00163
PRO_1000097294

Sites

Active site1341 By similarity
Metal binding911Iron By similarity
Metal binding1331Iron By similarity
Metal binding1371Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
B4S291 [UniParc].

Last modified September 23, 2008. Version 1.
Checksum: BD8480690C7AB1C9

FASTA16918,958
        10         20         30         40         50         60 
MAILDVLSFP DERLRTVAKP VEEVNDEIKQ LVSDMFETMK DENGIGLAAT QVNRHVQVVV 

        70         80         90        100        110        120 
MDVSEDQNEP RVFINPEITR KDGSTISEEG CLSVPGNYAK VERAEAITVK ALDQNGEAFE 

       130        140        150        160 
LDAEGLLAIC IQHELDHLKG KLFIDYLSPL KRQRIRKKLE KEARLAAKA 

« Hide

References

[1]"Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter."
Ivars-Martinez E., Martin-Cuadrado A.-B., D'Auria G., Mira A., Ferriera S., Johnson J., Friedman R., Rodriguez-Valera F.
ISME J. 2:1194-1212(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 17117 / Deep ecotype.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001103 Genomic DNA. Translation: AEA96170.1.
RefSeqYP_004425168.1. NC_011138.3.

3D structure databases

ProteinModelPortalB4S291.
SMRB4S291. Positions 1-164.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING314275.MADE_00022.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAEA96170; AEA96170; MADE_1000105.
GeneID6775476.
KEGGamc:MADE_1000105.
PATRIC20871297. VBIAltMac49397_0023.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
KOK01462.
OMAPNQYAEV.

Enzyme and pathway databases

BioCycAMAC314275:GHA7-21-MONOMER.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_ALTMD
AccessionPrimary (citable) accession number: B4S291
Secondary accession number(s): F2G1S3
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: May 14, 2014
This is version 42 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families