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Protein

Peptide deformylase 1

Gene

def1

Organism
Vibrio vulnificus (strain CMCP6)
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

BioCyciVVUL216895:GIYM-961-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:VV1_1048
OrganismiVibrio vulnificus (strain CMCP6)
Taxonomic identifieri216895 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002275 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylase 1PRO_0000082877Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi216895.VV1_1048.

Structurei

3D structure databases

ProteinModelPortaliQ8DDE3.
SMRiQ8DDE3. 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.

Q8DDE3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVLTFP DDRLRTVAKP VEKVTPEIQK IVDDMIETMY DEEGIGLAAT
60 70 80 90 100
QVDIHQRIVV IDISESRNEP MVLINPEILE KRGEDGIEEG CLSVPGARAL
110 120 130 140 150
VPRAAEVTVK ALDRDGHEFT LEADDLLAIC IQHELDHLQG KLFVDYLSPL
160 170
KRKRIQDKLA KIKRFNEKQR
Length:170
Mass (Da):19,293
Last modified:February 28, 2003 - v1
Checksum:iA03A4C710F0B3BC2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016795 Genomic DNA. Translation: AAO09535.1.
RefSeqiNP_760008.1. NC_004459.3.
WP_011079081.1. NC_004459.3.

Genome annotation databases

EnsemblBacteriaiAAO09535; AAO09535; VV1_1048.
GeneIDi1177981.
KEGGivvu:VV1_1048.
PATRICi20158909. VBIVibVul94426_1005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016795 Genomic DNA. Translation: AAO09535.1.
RefSeqiNP_760008.1. NC_004459.3.
WP_011079081.1. NC_004459.3.

3D structure databases

ProteinModelPortaliQ8DDE3.
SMRiQ8DDE3. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi216895.VV1_1048.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO09535; AAO09535; VV1_1048.
GeneIDi1177981.
KEGGivvu:VV1_1048.
PATRICi20158909. VBIVibVul94426_1005.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciVVUL216895:GIYM-961-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. "Complete genome sequence of Vibrio vulnificus CMCP6."
    Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E.
    Submitted (NOV-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CMCP6.

Entry informationi

Entry nameiDEF1_VIBVU
AccessioniPrimary (citable) accession number: Q8DDE3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 22, 2003
Last sequence update: February 28, 2003
Last modified: January 6, 2015
This is version 74 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

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.