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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)DescriptionActionsGraphical viewLength
Metal bindingi91IronUniRule annotation1
Metal bindingi133IronUniRule annotation1
Active sitei134UniRule annotation1
Metal bindingi137IronUniRule annotation1

GO - Molecular functioni

  • formylmethionine deformylase activity Source: TIGR
  • metal ion binding Source: UniProtKB-KW
  • peptide deformylase activity Source: GO_Central

GO - Biological processi

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
Proteomesi
  • UP000000584 Componenti: Chromosome 2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828741 – 168Peptide deformylase 2Add BLAST168

Interactioni

Protein-protein interaction databases

STRINGi243277.VCA0150.

Structurei

Secondary structure

1168
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 15Combined sources4
Helixi24 – 27Combined sources4
Helixi28 – 40Combined sources13
Beta strandi41 – 43Combined sources3
Beta strandi46 – 48Combined sources3
Helixi49 – 52Combined sources4
Beta strandi58 – 61Combined sources4
Beta strandi65 – 67Combined sources3
Beta strandi71 – 89Combined sources19
Beta strandi99 – 112Combined sources14
Beta strandi118 – 123Combined sources6
Helixi127 – 138Combined sources12
Helixi143 – 146Combined sources4
Helixi149 – 164Combined sources16

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9KN16.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
KOiK01462.
OMAiHYYQIVY.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3QU1X-ray1.80A/B1-168[»]
ProteinModelPortaliQ9KN16.
SMRiQ9KN16.
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

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
KOiK01462.
OMAiHYYQIVY.

Enzyme and pathway databases

BioCyciVCHO:VCA0150-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9KN16.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

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: November 2, 2016
This is version 90 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

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 one 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.