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Protein

Peptide deformylase 1

Gene

def1

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-3185-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:VP3042
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Peptide deformylase 1PRO_0000082875Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi223926.VP3042.

Structurei

3D structure databases

ProteinModelPortaliQ87KD5.
SMRiQ87KD5. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
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.

Q87KD5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVLTFP DDRLRTVAKP VDAVTPEIQK IVDDMIETMY DEEGIGLAAT
60 70 80 90 100
QVDIHKRIVV IDISETRDEP MVLINPEILE KRGEDGIEEG CLSVPGARAL
110 120 130 140 150
VPRAAEVTVK ALDRDGKEFT FEADDLLAIC VQHELDHLQG KLFVDYLSPL
160 170
KRKRIQDKLA KIKRFNEKQQ NA
Length:172
Mass (Da):19,405
Last modified:May 23, 2003 - v1
Checksum:i7B551ED4015A9E3C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC61305.1.
RefSeqiNP_799421.1. NC_004603.1.
WP_005461416.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC61305; BAC61305; BAC61305.
GeneIDi1190641.
KEGGivpa:VP3042.
PATRICi20144368. VBIVibPar50997_2927.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC61305.1.
RefSeqiNP_799421.1. NC_004603.1.
WP_005461416.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87KD5.
SMRiQ87KD5. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP3042.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC61305; BAC61305; BAC61305.
GeneIDi1190641.
KEGGivpa:VP3042.
PATRICi20144368. VBIVibPar50997_2927.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-3185-MONOMER.

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. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiDEF1_VIBPA
AccessioniPrimary (citable) accession number: Q87KD5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: May 23, 2003
Last modified: May 27, 2015
This is version 72 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

Complete proteome, Reference proteome

Documents

  1. 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.