Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Peptide deformylase

Gene

def

Organism
Helicobacter pylori (Campylobacter pylori)
Status
Unreviewed-Annotation score: Annotation score: 2 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 annotationSAAS annotation

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi96 – 961IronUniRule annotation
Metal bindingi138 – 1381IronUniRule annotation
Active sitei139 – 1391UniRule annotation
Metal bindingi142 – 1421IronUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

HydrolaseUniRule annotationSAAS annotation

Keywords - Biological processi

Protein biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

IronUniRule annotation, Metal-bindingUniRule annotationSAAS annotation

Enzyme and pathway databases

BRENDAi3.5.1.88. 2604.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotationSAAS annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotationImported
OrganismiHelicobacter pylori (Campylobacter pylori)Imported
Taxonomic identifieri210 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter

Interactioni

Protein-protein interaction databases

STRINGi85962.HP0793.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EW5X-ray2.20A2-174[»]
2EW6X-ray2.20A2-174[»]
2EW7X-ray2.20A2-174[»]
4E9AX-ray1.66A2-174[»]
4E9BX-ray1.70A2-164[»]
ProteinModelPortaliQ672W7.
SMRiQ672W7. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ672W7.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

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.

Q672W7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLEIIHYP SKILRTISKE VVSFDAKLHQ QLDDMYETMI ASEGIGLAAI
60 70 80 90 100
QVGLPLRMLI INLPQEDGVQ HKEDCLEIIN PKFIETGGSM MYKEGCLSVP
110 120 130 140 150
GFYEEVERFE KVKIEYQNRF AEVKVLEASE LLAVAIQHEI DHLNGVLFVD
160 170
KLSILKRKKF EKELKELQKK QKHK
Length:174
Mass (Da):20,038
Last modified:October 11, 2004 - v1
Checksum:iA10BEAEBE6CC4C85
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY559449 Genomic DNA. Translation: AAT51863.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY559449 Genomic DNA. Translation: AAT51863.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EW5X-ray2.20A2-174[»]
2EW6X-ray2.20A2-174[»]
2EW7X-ray2.20A2-174[»]
4E9AX-ray1.66A2-174[»]
4E9BX-ray1.70A2-164[»]
ProteinModelPortaliQ672W7.
SMRiQ672W7. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi85962.HP0793.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.5.1.88. 2604.

Miscellaneous databases

EvolutionaryTraceiQ672W7.

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. "Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori."
    Han C., Wang Q., Dong L., Sun H., Peng S., Chen J., Yang Y., Yue J., Shen X., Jiang H.
    Biochem. Biophys. Res. Commun. 319:1292-1298(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: SS1Imported.
  2. "Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation."
    Cai J., Han C., Hu T., Zhang J., Wu D., Wang F., Liu Y., Ding J., Chen K., Yue J., Shen X., Jiang H.
    Protein Sci. 15:2071-2081(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 2-174.
  3. "Identification of Novel Peptide Deformylase Inhibitors from Natural Products."
    Cui K., Zhu L., Lu W., Huang J.
    Submitted (MAR-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF 2-174.

Entry informationi

Entry nameiQ672W7_HELPX
AccessioniPrimary (citable) accession number: Q672W7
Entry historyi
Integrated into UniProtKB/TrEMBL: October 11, 2004
Last sequence update: October 11, 2004
Last modified: June 24, 2015
This is version 54 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

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.