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Protein

Peptide deformylase

Gene

def

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 bindingi92IronUniRule annotation1
Metal bindingi134IronUniRule annotation1
Active sitei135UniRule annotation1
Metal bindingi138IronUniRule annotation1

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

BRENDAi3.5.1.88. 5087.

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:PA0019
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA0019.

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1649054.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828191 – 168Peptide deformylaseAdd BLAST168

Proteomic databases

PaxDbiQ9I7A8.
PRIDEiQ9I7A8.

Interactioni

Protein-protein interaction databases

STRINGi208964.PA0019.

Chemistry databases

BindingDBiQ9I7A8.

Structurei

Secondary structure

1168
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 15Combined sources4
Helixi26 – 41Combined sources16
Beta strandi45 – 48Combined sources4
Helixi49 – 52Combined sources4
Beta strandi56 – 62Combined sources7
Beta strandi64 – 67Combined sources4
Beta strandi70 – 81Combined sources12
Beta strandi85 – 90Combined sources6
Beta strandi100 – 106Combined sources7
Beta strandi108 – 113Combined sources6
Beta strandi119 – 124Combined sources6
Helixi126 – 139Combined sources14
Helixi144 – 147Combined sources4
Helixi150 – 166Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IX1X-ray1.85A/B1-168[»]
1LRYX-ray2.60A2-168[»]
1N5NX-ray1.80A/B1-168[»]
1S17X-ray1.95A/B1-168[»]
ProteinModelPortaliQ9I7A8.
SMRiQ9I7A8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9I7A8.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
InParanoidiQ9I7A8.
KOiK01462.
OMAiVCIQHEI.
PhylomeDBiQ9I7A8.

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.

Q9I7A8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAILNILEFP DPRLRTIAKP VEVVDDAVRQ LIDDMFETMY EAPGIGLAAT
60 70 80 90 100
QVNVHKRIVV MDLSEDKSEP RVFINPEFEP LTEDMDQYQE GCLSVPGFYE
110 120 130 140 150
NVDRPQKVRI KALDRDGNPF EEVAEGLLAV CIQHECDHLN GKLFVDYLST
160
LKRDRIRKKL EKQHRQQA
Length:168
Mass (Da):19,365
Last modified:March 1, 2001 - v1
Checksum:iA95F6B921E5F3189
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA. Translation: AAG03409.1.
PIRiH83643.
RefSeqiNP_248709.1. NC_002516.2.
WP_003107059.1. NZ_ASJY01000003.1.

Genome annotation databases

EnsemblBacteriaiAAG03409; AAG03409; PA0019.
GeneIDi879306.
KEGGipae:PA0019.
PATRICi19834232. VBIPseAer58763_0018.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA. Translation: AAG03409.1.
PIRiH83643.
RefSeqiNP_248709.1. NC_002516.2.
WP_003107059.1. NZ_ASJY01000003.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IX1X-ray1.85A/B1-168[»]
1LRYX-ray2.60A2-168[»]
1N5NX-ray1.80A/B1-168[»]
1S17X-ray1.95A/B1-168[»]
ProteinModelPortaliQ9I7A8.
SMRiQ9I7A8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA0019.

Chemistry databases

BindingDBiQ9I7A8.
ChEMBLiCHEMBL1649054.

Proteomic databases

PaxDbiQ9I7A8.
PRIDEiQ9I7A8.

Protocols and materials databases

DNASUi879306.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG03409; AAG03409; PA0019.
GeneIDi879306.
KEGGipae:PA0019.
PATRICi19834232. VBIPseAer58763_0018.

Organism-specific databases

PseudoCAPiPA0019.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
InParanoidiQ9I7A8.
KOiK01462.
OMAiVCIQHEI.
PhylomeDBiQ9I7A8.

Enzyme and pathway databases

BRENDAi3.5.1.88. 5087.

Miscellaneous databases

EvolutionaryTraceiQ9I7A8.

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_PSEAE
AccessioniPrimary (citable) accession number: Q9I7A8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: March 1, 2001
Last modified: November 2, 2016
This is version 111 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.