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Q8DDE3

- DEF1_VIBVU

UniProt

Q8DDE3 - DEF1_VIBVU

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Protein

Peptide deformylase 1

Gene
def1, VV1_1048
Organism
Vibrio vulnificus (strain CMCP6)
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

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylase 1UniRule annotationPRO_0000082877Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi216895.VV1_1048.

Structurei

3D structure databases

ProteinModelPortaliQ8DDE3.
SMRiQ8DDE3. 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.

Q8DDE3-1 [UniParc]FASTAAdd to Basket

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MSVLQVLTFP DDRLRTVAKP VEKVTPEIQK IVDDMIETMY DEEGIGLAAT    50
QVDIHQRIVV IDISESRNEP MVLINPEILE KRGEDGIEEG CLSVPGARAL 100
VPRAAEVTVK ALDRDGHEFT LEADDLLAIC IQHELDHLQG KLFVDYLSPL 150
KRKRIQDKLA KIKRFNEKQR 170
Length:170
Mass (Da):19,293
Last modified:March 1, 2003 - v1
Checksum:iA03A4C710F0B3BC2
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AE016795 Genomic DNA. Translation: AAO09535.1 .
RefSeqi NP_760008.1. NC_004459.3.
WP_011079081.1. NC_004459.3.

3D structure databases

ProteinModelPortali Q8DDE3.
SMRi Q8DDE3. Positions 2-168.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 216895.VV1_1048.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAO09535 ; AAO09535 ; VV1_1048 .
GeneIDi 1177981.
KEGGi vvu:VV1_1048.
PATRICi 20158909. VBIVibVul94426_1005.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci VVUL216895:GIYM-961-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. "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 (DEC-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 23, 2003
Last sequence update: March 1, 2003
Last modified: September 3, 2014
This is version 70 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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