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Protein

Peptide deformylase

Gene

def

Organism
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
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 bindingi92 – 921IronUniRule annotation
Metal bindingi134 – 1341IronUniRule annotation
Active sitei135 – 1351UniRule annotation
Metal bindingi138 – 1381IronUniRule 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

BioCyciSDEG203122:GI2M-21-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:Sde_0021
OrganismiSaccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Taxonomic identifieri203122 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesAlteromonadaceaeSaccharophagus
ProteomesiUP000001947 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Peptide deformylasePRO_0000301092Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi203122.Sde_0021.

Structurei

3D structure databases

ProteinModelPortaliQ21PV5.
SMRiQ21PV5. Positions 1-166.
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.

Q21PV5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLPILEFP DPRLRTIAKP VAKVDQRIRT LIDDMFETMY DAPGIGLAAT
60 70 80 90 100
QVNVHEQVLV IDLGEETKEP MVFINPSIEI LDQEHYEYEE GCLSVPGFYE
110 120 130 140 150
QVSRPKHIRV TALDRDGKEF VIEPEGLLAV CVQHEMDHLN GKLFVDYVSN
160 170
IKRQRIRKKL EKQHRQAAQS VG
Length:172
Mass (Da):19,706
Last modified:April 18, 2006 - v1
Checksum:i5BDA3D66CE356F49
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000282 Genomic DNA. Translation: ABD79285.1.
RefSeqiWP_011466509.1. NC_007912.1.
YP_525497.1. NC_007912.1.

Genome annotation databases

EnsemblBacteriaiABD79285; ABD79285; Sde_0021.
KEGGisde:Sde_0021.
PATRICi23398627. VBISacDeg56404_0022.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000282 Genomic DNA. Translation: ABD79285.1.
RefSeqiWP_011466509.1. NC_007912.1.
YP_525497.1. NC_007912.1.

3D structure databases

ProteinModelPortaliQ21PV5.
SMRiQ21PV5. Positions 1-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi203122.Sde_0021.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD79285; ABD79285; Sde_0021.
KEGGisde:Sde_0021.
PATRICi23398627. VBISacDeg56404_0022.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciSDEG203122:GI2M-21-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: 2-40 / ATCC 43961 / DSM 17024.

Entry informationi

Entry nameiDEF_SACD2
AccessioniPrimary (citable) accession number: Q21PV5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: April 18, 2006
Last modified: May 27, 2015
This is version 63 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.