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Protein

Peptide deformylase 1

Gene

def1

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule annotation

GO - Molecular functioni

  1. formylmethionine deformylase activity Source: TIGR
  2. iron ion binding Source: InterPro
  3. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. cellular protein modification process Source: TIGR
  2. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciVCHO:VC0046-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
Ordered Locus Names:VC_0046
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000000584 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 169169Peptide deformylase 1PRO_0000082873Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi243277.VC0046.

Structurei

Secondary structure

1
169
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 154Combined sources
Helixi26 – 4116Combined sources
Beta strandi45 – 484Combined sources
Helixi49 – 524Combined sources
Beta strandi56 – 616Combined sources
Beta strandi71 – 8313Combined sources
Beta strandi85 – 895Combined sources
Beta strandi99 – 1035Combined sources
Beta strandi105 – 1128Combined sources
Beta strandi118 – 1236Combined sources
Helixi125 – 13814Combined sources
Helixi143 – 1464Combined sources
Helixi149 – 16315Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FWXX-ray2.00A/B1-169[»]
ProteinModelPortaliQ9KVU3.
SMRiQ9KVU3. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KVU3.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9KVU3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT
60 70 80 90 100
QVDIHQRIVV IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL
110 120 130 140 150
VPRAAEVTVK ALDRNGQEYQ FDADDLLAIC VQHELDHLAG KLFVDYLSPL
160
KRNRIKEKLE KIKRFNEKK
Length:169
Mass (Da):19,147
Last modified:October 1, 2000 - v1
Checksum:i16DB00B08CA40FC7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF93224.1.
PIRiA82373.
RefSeqiNP_229705.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF93224; AAF93224; VC_0046.
GeneIDi2614445.
KEGGivch:VC0046.
PATRICi20079140. VBIVibCho83274_0045.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF93224.1.
PIRiA82373.
RefSeqiNP_229705.1. NC_002505.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FWXX-ray2.00A/B1-169[»]
ProteinModelPortaliQ9KVU3.
SMRiQ9KVU3. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC0046.

Protocols and materials databases

DNASUi2614445.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF93224; AAF93224; VC_0046.
GeneIDi2614445.
KEGGivch:VC0046.
PATRICi20079140. VBIVibCho83274_0045.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciVCHO:VC0046-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9KVU3.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39315 / El Tor Inaba N16961.

Entry informationi

Entry nameiDEF1_VIBCH
AccessioniPrimary (citable) accession number: Q9KVU3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: October 1, 2000
Last modified: January 7, 2015
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.