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Protein

Peptide deformylase

Gene

def

Organism
Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
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)DescriptionActionsGraphical viewLength
Metal bindingi99IronUniRule annotation1
Metal bindingi141IronUniRule annotation1
Active sitei142UniRule annotation1
Metal bindingi145IronUniRule annotation1

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 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:Swit_4045
OrganismiSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
Taxonomic identifieri392499 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas
Proteomesi
  • UP000001989 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000231351 – 177Peptide deformylaseAdd BLAST177

Interactioni

Protein-protein interaction databases

STRINGi392499.Swit_4045.

Structurei

3D structure databases

ProteinModelPortaliA5VDM3.
SMRiA5VDM3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
KOiK01462.
OMAiVCIQHEI.
OrthoDBiPOG091H02B0.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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.

A5VDM3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIRLILEAP DPRLRTISTP VEAVDDELRA LIADMFETMY DAPGIGLAAI
60 70 80 90 100
QVGVPKRVLV IDLQEEEDAE GKPIRHPRVF INPELFDPSE EQSVYNEGCL
110 120 130 140 150
SVPEQYAEVE RPAVIHARWL DEQGAKHEER LEGLLATCLQ HEMDHLEGIL
160 170
FIDHLSRLKR EMVMKKLEKA RRARKAA
Length:177
Mass (Da):20,154
Last modified:July 10, 2007 - v1
Checksum:i1A62E4EA8CF88867
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000699 Genomic DNA. Translation: ABQ70389.1.
RefSeqiWP_012050228.1. NC_009511.1.

Genome annotation databases

EnsemblBacteriaiABQ70389; ABQ70389; Swit_4045.
KEGGiswi:Swit_4045.
PATRICi23687377. VBISphWit55028_4617.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000699 Genomic DNA. Translation: ABQ70389.1.
RefSeqiWP_012050228.1. NC_009511.1.

3D structure databases

ProteinModelPortaliA5VDM3.
SMRiA5VDM3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi392499.Swit_4045.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ70389; ABQ70389; Swit_4045.
KEGGiswi:Swit_4045.
PATRICi23687377. VBISphWit55028_4617.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
KOiK01462.
OMAiVCIQHEI.
OrthoDBiPOG091H02B0.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

Entry informationi

Entry nameiDEF_SPHWW
AccessioniPrimary (citable) accession number: A5VDM3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 10, 2007
Last modified: November 2, 2016
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

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 one 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.