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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: -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

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, 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
Proteomesi
  • UP000000584 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828731 – 169Peptide deformylase 1Add BLAST169

Proteomic databases

PRIDEiQ9KVU3

Interactioni

Protein-protein interaction databases

STRINGi243277.VC0046

Structurei

Secondary structure

1169
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 15Combined sources4
Helixi26 – 41Combined sources16
Beta strandi45 – 48Combined sources4
Helixi49 – 52Combined sources4
Beta strandi56 – 61Combined sources6
Beta strandi71 – 83Combined sources13
Beta strandi85 – 89Combined sources5
Beta strandi99 – 103Combined sources5
Beta strandi105 – 112Combined sources8
Beta strandi118 – 123Combined sources6
Helixi125 – 138Combined sources14
Helixi143 – 146Combined sources4
Helixi149 – 163Combined sources15

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9KVU3

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
KOiK01462
OMAiVCIQHEI

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
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
WP_000115010.1, NC_002505.1

Genome annotation databases

EnsemblBacteriaiAAF93224; AAF93224; VC_0046
GeneIDi2614445
KEGGivch:VC0046
PATRICifig|243277.26.peg.45

Similar proteinsi

Entry informationi

Entry nameiDEF1_VIBCH
AccessioniPrimary (citable) accession number: Q9KVU3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: October 1, 2000
Last modified: May 23, 2018
This is version 101 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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