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Q21PV5 (DEF_SACD2) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 56. 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:Sde_0021
OrganismSaccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) [Complete proteome] [HAMAP]
Taxonomic identifier203122 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesAlteromonadaceaeSaccharophagus

Protein attributes

Sequence length172 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 – 172172Peptide deformylase HAMAP-Rule MF_00163
PRO_0000301092

Sites

Active site1351 By similarity
Metal binding921Iron By similarity
Metal binding1341Iron By similarity
Metal binding1381Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
Q21PV5 [UniParc].

Last modified April 18, 2006. Version 1.
Checksum: 5BDA3D66CE356F49

FASTA17219,706
        10         20         30         40         50         60 
MALLPILEFP DPRLRTIAKP VAKVDQRIRT LIDDMFETMY DAPGIGLAAT QVNVHEQVLV 

        70         80         90        100        110        120 
IDLGEETKEP MVFINPSIEI LDQEHYEYEE GCLSVPGFYE QVSRPKHIRV TALDRDGKEF 

       130        140        150        160        170 
VIEPEGLLAV CVQHEMDHLN GKLFVDYVSN IKRQRIRKKL EKQHRQAAQS VG 

« Hide

References

[1]"Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T."
Weiner R.M., Taylor L.E. II, Henrissat B., Hauser L., Land M., Coutinho P.M., Rancurel C., Saunders E.H., Longmire A.G., Zhang H., Bayer E.A., Gilbert H.J., Larimer F., Zhulin I.B., Ekborg N.A., Lamed R., Richardson P.M., Borovok I., Hutcheson S.
PLoS Genet. 4:E1000087-E1000087(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 2-40 / ATCC 43961 / DSM 17024.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000282 Genomic DNA. Translation: ABD79285.1.
RefSeqYP_525497.1. NC_007912.1.

3D structure databases

ProteinModelPortalQ21PV5.
SMRQ21PV5. Positions 1-166.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING203122.Sde_0021.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABD79285; ABD79285; Sde_0021.
GeneID3968154.
KEGGsde:Sde_0021.
PATRIC23398627. VBISacDeg56404_0022.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMATIMYKEG.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycSDEG203122:GI2M-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_SACD2
AccessionPrimary (citable) accession number: Q21PV5
Entry history
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: April 18, 2006
Last modified: May 14, 2014
This is version 56 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