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Protein

Peptide deformylase 2

Gene

def2

Organism
Shewanella oneidensis (strain MR-1)
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 bindingi109 – 1091IronUniRule annotation
Metal bindingi151 – 1511IronUniRule annotation
Active sitei152 – 1521UniRule annotation
Metal bindingi155 – 1551IronUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

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:SO_1062
OrganismiShewanella oneidensis (strain MR-1)
Taxonomic identifieri211586 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
ProteomesiUP000008186 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 181181Peptide deformylase 2PRO_0000082835Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi211586.SO_1062.

Structurei

3D structure databases

ProteinModelPortaliQ8EHZ2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiERSQMPE.
OrthoDBiEOG664CMF.
PhylomeDBiQ8EHZ2.

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.

Q8EHZ2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFKDEMRQTP NKPLPIAVVG EAILKQQAIE VRDFDDTLSQ LASQMAASMV
60 70 80 90 100
EAKGVGIAAP QVHSPLALFI MASRPNERYP DAPLMEPLVV VNPQIVLRSL
110 120 130 140 150
QLEKGEEGCL SVPGQRFTIW RPQTIVVRYQ NLAGQWQHSE LTGFIARIFQ
160 170 180
HEFDHLQGIT LLERSQMPEQ KLMAQEGKPQ A
Length:181
Mass (Da):20,325
Last modified:March 1, 2003 - v1
Checksum:iBF5C27BADEA587C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014299 Genomic DNA. Translation: AAN54134.1.
RefSeqiNP_716689.1. NC_004347.2.
WP_011071316.1. NC_004347.2.

Genome annotation databases

EnsemblBacteriaiAAN54134; AAN54134; SO_1062.
GeneIDi1168899.
KEGGison:SO_1062.
PATRICi23521771. VBISheOne101494_1019.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014299 Genomic DNA. Translation: AAN54134.1.
RefSeqiNP_716689.1. NC_004347.2.
WP_011071316.1. NC_004347.2.

3D structure databases

ProteinModelPortaliQ8EHZ2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi211586.SO_1062.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN54134; AAN54134; SO_1062.
GeneIDi1168899.
KEGGison:SO_1062.
PATRICi23521771. VBISheOne101494_1019.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiERSQMPE.
OrthoDBiEOG664CMF.
PhylomeDBiQ8EHZ2.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MR-1.

Entry informationi

Entry nameiDEF2_SHEON
AccessioniPrimary (citable) accession number: Q8EHZ2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2003
Last sequence update: March 1, 2003
Last modified: April 29, 2015
This is version 79 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.