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Q87KD5

- DEF1_VIBPA

UniProt

Q87KD5 - DEF1_VIBPA

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Protein

Peptide deformylase 1

Gene
def1, VP3042
Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed - 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 By similarity.UniRule annotation

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Binds 1 Fe2+ ion By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911Iron By similarity
Metal bindingi133 – 1331Iron By similarity
Active sitei134 – 1341 By similarity
Metal bindingi137 – 1371Iron By similarity

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:GHK4-3185-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1 (EC:3.5.1.88)
Short name:
PDF 1
Alternative name(s):
Polypeptide deformylase 1
Gene namesi
Name:def1
Ordered Locus Names:VP3042
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Peptide deformylase 1UniRule annotationPRO_0000082875Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi223926.VP3042.

Structurei

3D structure databases

ProteinModelPortaliQ87KD5.
SMRiQ87KD5. Positions 2-168.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiELLAICI.
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

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MSVLQVLTFP DDRLRTVAKP VDAVTPEIQK IVDDMIETMY DEEGIGLAAT    50
QVDIHKRIVV IDISETRDEP MVLINPEILE KRGEDGIEEG CLSVPGARAL 100
VPRAAEVTVK ALDRDGKEFT FEADDLLAIC VQHELDHLQG KLFVDYLSPL 150
KRKRIQDKLA KIKRFNEKQQ NA 172
Length:172
Mass (Da):19,405
Last modified:May 23, 2003 - v1
Checksum:i7B551ED4015A9E3C
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000031 Genomic DNA. Translation: BAC61305.1.
RefSeqiNP_799421.1. NC_004603.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000031 Genomic DNA. Translation: BAC61305.1 .
RefSeqi NP_799421.1. NC_004603.1.

3D structure databases

ProteinModelPortali Q87KD5.
SMRi Q87KD5. Positions 2-168.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 223926.VP3042.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAC61305 ; BAC61305 ; BAC61305 .
GeneIDi 1190641.
KEGGi vpa:VP3042.
PATRICi 20144368. VBIVibPar50997_2927.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
KOi K01462.
OMAi ELLAICI.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci VPAR223926:GHK4-3185-MONOMER.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PIRSFi PIRSF004749. Pep_def. 1 hit.
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

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 14, 2014
This is version 68 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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