Skip Header

Contribute Send feedback
Read comments (?) or add your own

Q7MCQ2 (DEF1_VIBVY) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 62. 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
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 1
Short name=PDF 1
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase 1
Gene names
Name:def1
Ordered Locus Names:VVA1334
OrganismVibrio vulnificus (strain YJ016) [Complete proteome] [HAMAP]
Taxonomic identifier196600 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio ›

Protein attributes

Sequence length168 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: HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 168168Peptide deformylase 1 HAMAP-Rule MF_00163
PRO_0000082879

Sites

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

Sequences

Sequence LengthMass (Da)Tools
Q7MCQ2 [UniParc].

Last modified December 15, 2003. Version 1.
Checksum: 223FCB42ECE863B1

FASTA16818,760
        10         20         30         40         50         60 
MAVLEILTAP DPRLRVQSKE VTDVAAVQTL IDDLLETLYE TDNGVGLAAP QVGREEAIVV 

        70         80         90        100        110        120 
IDLSENRDEP LVLVNPKVVS GSNKEMGQEG CLSVPDYYAD VERYTSVVVE ALDRNGKELR 

       130        140        150        160 
IETSEFLAIV MQHEIDHLSG NLFIDYLSPL KQQMAMKKVK KHNKLRAR

« Hide

References

[1]"Comparative genome analysis of Vibrio vulnificus, a marine pathogen."
Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L., Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P., Lee C.-T., Hor L.-I., Tsai S.-F.
Genome Res. 13:2577-2587(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: YJ016.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		BA000038 Genomic DNA. Translation: BAC97360.1.
RefSeqNP_937390.1. NC_005140.1.

3D structure databases

ProteinModelPortalQ7MCQ2.
SMRQ7MCQ2. Positions 2-168.
ModBaseSearch...

Protein-protein interaction databases

STRING196600.VVA1334.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAC97360; BAC97360; BAC97360.
GeneID2622196.
KEGGvvy:VVA1334.
PATRIC20175960. VBIVibVul40472_4481.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMARVQSKEV.
ProtClustDBPRK12846.

Enzyme and pathway databases

BioCycVVUL196600:GJ9W-4734-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. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF1_VIBVY
AccessionPrimary (citable) accession number: Q7MCQ2
Entry history
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: December 15, 2003
Last modified: May 29, 2013
This is version 62 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

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents