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Q8DDE3 (DEF1_VIBVU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 68. 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 1

Short name=PDF 1
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase 1
Gene names
Name:def1
Ordered Locus Names:VV1_1048
OrganismVibrio vulnificus (strain CMCP6) [Complete proteome] [HAMAP]
Taxonomic identifier216895 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio

Protein attributes

Sequence length170 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 – 170170Peptide deformylase 1 HAMAP-Rule MF_00163
PRO_0000082877

Sites

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

Sequences

Sequence LengthMass (Da)Tools
Q8DDE3 [UniParc].

Last modified March 1, 2003. Version 1.
Checksum: A03A4C710F0B3BC2

FASTA17019,293
        10         20         30         40         50         60 
MSVLQVLTFP DDRLRTVAKP VEKVTPEIQK IVDDMIETMY DEEGIGLAAT QVDIHQRIVV 

        70         80         90        100        110        120 
IDISESRNEP MVLINPEILE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRDGHEFT 

       130        140        150        160        170 
LEADDLLAIC IQHELDHLQG KLFVDYLSPL KRKRIQDKLA KIKRFNEKQR 

« Hide

References

[1]"Complete genome sequence of Vibrio vulnificus CMCP6."
Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E.
Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CMCP6.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE016795 Genomic DNA. Translation: AAO09535.1.
RefSeqNP_760008.1. NC_004459.3.

3D structure databases

ProteinModelPortalQ8DDE3.
SMRQ8DDE3. Positions 2-168.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING216895.VV1_1048.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAO09535; AAO09535; VV1_1048.
GeneID1177981.
KEGGvvu:VV1_1048.
PATRIC20158909. VBIVibVul94426_1005.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAMAETMYE.
OrthoDBEOG664CMF.
ProtClustDBPRK00150.

Enzyme and pathway databases

BioCycVVUL216895:GIYM-961-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 nameDEF1_VIBVU
AccessionPrimary (citable) accession number: Q8DDE3
Entry history
Integrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: March 1, 2003
Last modified: February 19, 2014
This is version 68 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