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Q9KVU3 (DEF1_VIBCH) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 68. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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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:VC_0046
OrganismVibrio cholerae
Taxonomic identifier666 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length169 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

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 MF_00163

Catalytic activity

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

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP MF_00163

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological processtranslation

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 169169Peptide deformylase 1 HAMAP MF_00163
PRO_0000082873

Sites

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

Secondary structure

1 ....................... 169
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9KVU3 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 16DB00B08CA40FC7

FASTA16919,147
        10         20         30         40         50         60 
MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT QVDIHQRIVV 

        70         80         90        100        110        120 
IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRNGQEYQ 

       130        140        150        160 
FDADDLLAIC VQHELDHLAG KLFVDYLSPL KRNRIKEKLE KIKRFNEKK

« Hide

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE003852 Genomic DNA. Translation: AAF93224.1.
PIRA82373.
RefSeqNP_229705.1. NC_002505.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3FWXX-ray2.00A/B1-169[»]
ProteinModelPortalQ9KVU3.
SMRQ9KVU3. Positions 2-168.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID2614445.
GenomeReviewsGene locus VC_0046 in contig AE003852_GR.
KEGGvch:VC0046.
PATRIC20079140. VBIVibCho83274_0045.
TIGRVC_0046.

Phylogenomic databases

HOGENOMHBG665227.
OMAQKIVDDM.
PhylomeDBQ9KVU3.
ProtClustDBPRK00150.

Family and domain databases

HAMAPMF_00163. Pep_deformylase.
[Tree]
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
KOK01462.
PANTHERPTHR10458. Fmet_deformylase. 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_VIBCH
AccessionPrimary (citable) accession number: Q9KVU3
Entry history
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: October 1, 2000
Last modified: January 25, 2012
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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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