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Protein

Peptide deformylase

Gene

def

Organism
Salinibacter ruber (strain DSM 13855 / M31)
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 bindingi102 – 1021IronUniRule annotation
Metal bindingi144 – 1441IronUniRule annotation
Active sitei145 – 1451UniRule annotation
Metal bindingi148 – 1481IronUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciSRUB309807:GJJD-1288-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:SRU_1291
OrganismiSalinibacter ruber (strain DSM 13855 / M31)
Taxonomic identifieri309807 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidetes Order II. Incertae sedisRhodothermaceaeSalinibacter
ProteomesiUP000008674 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 195195Peptide deformylasePRO_0000301093Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi309807.SRU_1291.

Structurei

3D structure databases

ProteinModelPortaliQ2S316.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.
PhylomeDBiQ2S316.

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.

Q2S316-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILPIYVYGH EALRNETDPV QENTEALQEL IDNMIETMHN AAGIGLAAPQ
60 70 80 90 100
VGRTERLFVV DLTPMADEIA EAGEPLPPQP MVFINPEIVE ESEDTAEMEE
110 120 130 140 150
GCLSIPEVRE AVARPERIRM RYRDREFEEQ ELEAGGMLSR VLQHERDHLD
160 170 180 190
GVLFTDYLSS FRKRLLRRPL REMVNGEVEA DYPLVTKDDE TVPSR
Length:195
Mass (Da):22,304
Last modified:January 24, 2006 - v1
Checksum:iCAFDB2D715C7AF82
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000159 Genomic DNA. Translation: ABC46292.1.
RefSeqiWP_011404043.1. NC_007677.1.
YP_445415.1. NC_007677.1.

Genome annotation databases

EnsemblBacteriaiABC46292; ABC46292; SRU_1291.
GeneIDi3851213.
KEGGisru:SRU_1291.
PATRICi23425005. VBISalRub86502_1342.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000159 Genomic DNA. Translation: ABC46292.1.
RefSeqiWP_011404043.1. NC_007677.1.
YP_445415.1. NC_007677.1.

3D structure databases

ProteinModelPortaliQ2S316.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi309807.SRU_1291.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABC46292; ABC46292; SRU_1291.
GeneIDi3851213.
KEGGisru:SRU_1291.
PATRICi23425005. VBISalRub86502_1342.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.
PhylomeDBiQ2S316.

Enzyme and pathway databases

BioCyciSRUB309807:GJJD-1288-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 13855 / M31.

Entry informationi

Entry nameiDEF_SALRD
AccessioniPrimary (citable) accession number: Q2S316
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: January 24, 2006
Last modified: July 22, 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.