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Protein

Peptide deformylase 2

Gene

def2

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

  • formylmethionine deformylase activity Source: TIGR
  • iron ion binding Source: InterPro
  • peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  • cellular protein modification process Source: TIGR
  • 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:VCA0150-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 2UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 2UniRule annotation
Alternative name(s):
Polypeptide deformylase 2UniRule annotation
Gene namesi
Name:def2UniRule annotation
Ordered Locus Names:VC_A0150
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000000584 Componenti: Chromosome 2

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 168168Peptide deformylase 2PRO_0000082874Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi243277.VCA0150.

Structurei

Secondary structure

1
168
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 154Combined sources
Helixi24 – 274Combined sources
Helixi28 – 4013Combined sources
Beta strandi41 – 433Combined sources
Beta strandi46 – 483Combined sources
Helixi49 – 524Combined sources
Beta strandi58 – 614Combined sources
Beta strandi65 – 673Combined sources
Beta strandi71 – 8919Combined sources
Beta strandi99 – 11214Combined sources
Beta strandi118 – 1236Combined sources
Helixi127 – 13812Combined sources
Helixi143 – 1464Combined sources
Helixi149 – 16416Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3QU1X-ray1.80A/B1-168[»]
ProteinModelPortaliQ9KN16.
SMRiQ9KN16. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KN16.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiTIWGEPV.
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.

Q9KN16-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVLEILTAP DPRLRVQSKQ VTDVASVQTL IDDLLDTLYA TDNGIGLAAP
60 70 80 90 100
QVGREEAIVV IDLSDNRDQP LVLINPKVVS GSNKEMGQEG CLSVPDYYAD
110 120 130 140 150
VERYTSVVVE ALDREGKPLR IETSDFLAIV MQHEIDHLSG NLFIDYLSPL
160
KQQMAMKKVK KHVKNRAR
Length:168
Mass (Da):18,671
Last modified:October 1, 2000 - v1
Checksum:iF51EDDE3B6C14C59
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003853 Genomic DNA. Translation: AAF96063.1.
PIRiC82494.
RefSeqiNP_232550.1. NC_002506.1.
WP_000279461.1. NC_002506.1.

Genome annotation databases

EnsemblBacteriaiAAF96063; AAF96063; VC_A0150.
GeneIDi2612555.
KEGGivch:VCA0150.
PATRICi20084873. VBIVibCho83274_2788.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003853 Genomic DNA. Translation: AAF96063.1.
PIRiC82494.
RefSeqiNP_232550.1. NC_002506.1.
WP_000279461.1. NC_002506.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3QU1X-ray1.80A/B1-168[»]
ProteinModelPortaliQ9KN16.
SMRiQ9KN16. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VCA0150.

Protocols and materials databases

DNASUi2612555.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF96063; AAF96063; VC_A0150.
GeneIDi2612555.
KEGGivch:VCA0150.
PATRICi20084873. VBIVibCho83274_2788.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiTIWGEPV.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciVCHO:VCA0150-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9KN16.

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 nameiDEF2_VIBCH
AccessioniPrimary (citable) accession number: Q9KN16
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: October 1, 2000
Last modified: May 27, 2015
This is version 81 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.