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Protein

Peptide deformylase 2

Gene

def2

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

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

GO - Biological processi

  1. 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

BioCyciVPAR223926:GHK4-4017-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:VPA0784
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493 Componenti: Chromosome 2

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 168168Peptide deformylase 2PRO_0000082876Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi223926.VPA0784.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
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.

Q87I22-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVLEILSIP DPRLKVKAEK VTDVSTIQTL IDDMLETLYA TGNGIGLAST
60 70 80 90 100
QVGRKEAVVV IDISDERNDP LILVNPEVVS GENKALGQEG CLSVPEYYAD
110 120 130 140 150
VERYTSVVVS ALDRDGNPIT IESDEFLAIV MQHEIDHLSG NLFIDYLSPL
160
KQKMAMKKVK KYVKAQAK
Length:168
Mass (Da):18,491
Last modified:May 23, 2003 - v1
Checksum:iD71655F48CE28EE6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA. Translation: BAC62127.1.
RefSeqiNP_800294.1. NC_004605.1.

Genome annotation databases

EnsemblBacteriaiBAC62127; BAC62127; BAC62127.
GeneIDi1191473.
KEGGivpa:VPA0784.
PATRICi20145969. VBIVibPar50997_3717.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA. Translation: BAC62127.1.
RefSeqiNP_800294.1. NC_004605.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VPA0784.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC62127; BAC62127; BAC62127.
GeneIDi1191473.
KEGGivpa:VPA0784.
PATRICi20145969. VBIVibPar50997_3717.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiTIWGEPV.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-4017-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(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiDEF2_VIBPA
AccessioniPrimary (citable) accession number: Q87I22
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: May 23, 2003
Last modified: April 1, 2015
This is version 71 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.