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Protein

Peptide deformylase

Gene

def

Organism
Haemophilus influenzae (strain 86-028NP)
Status
Reviewed-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 annotation

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi91IronUniRule annotation1
Metal bindingi133IronUniRule annotation1
Active sitei134UniRule annotation1
Metal bindingi137IronUniRule 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

BioCyciHINF281310:GJ89-685-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:NTHI0725
OrganismiHaemophilus influenzae (strain 86-028NP)
Taxonomic identifieri281310 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
Proteomesi
  • UP000002525 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003010351 – 169Peptide deformylaseAdd BLAST169

Structurei

Secondary structure

1169
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 14Combined sources3
Helixi26 – 41Combined sources16
Beta strandi45 – 48Combined sources4
Helixi49 – 52Combined sources4
Beta strandi56 – 61Combined sources6
Beta strandi63 – 69Combined sources7
Beta strandi71 – 82Combined sources12
Beta strandi88 – 91Combined sources4
Beta strandi94 – 100Combined sources7
Beta strandi105 – 112Combined sources8
Beta strandi118 – 123Combined sources6
Helixi125 – 138Combined sources14
Helixi143 – 146Combined sources4
Helixi149 – 165Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4WXKX-ray2.05A/B/C/D1-169[»]
4WXLX-ray2.33A/B/C/D1-169[»]
ProteinModelPortaliQ4QMV6.
SMRiQ4QMV6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

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.

Q4QMV6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTALNVLIYP DDHLKVVCEP VTEVNDAIRK IVDDMFDTMY QEKGIGLAAP
60 70 80 90 100
QVDILQRIIT IDVEGDKQNQ FVLINPEILA SEGETGIEEG CLSIPGFRAL
110 120 130 140 150
VPRKEKVTVR ALDRDGKEFT LDADGLLAIC IQHEIDHLNG ILFVDYLSPL
160
KRQRIKEKLI KYKKQIAKS
Length:169
Mass (Da):19,058
Last modified:July 19, 2005 - v1
Checksum:i7040E05554F738CD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000057 Genomic DNA. Translation: AAX87641.1.
RefSeqiWP_005630900.1. NC_007146.2.

Genome annotation databases

EnsemblBacteriaiAAX87641; AAX87641; NTHI0725.
KEGGihit:NTHI0725.
PATRICi20181609. VBIHaeInf100748_0674.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000057 Genomic DNA. Translation: AAX87641.1.
RefSeqiWP_005630900.1. NC_007146.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4WXKX-ray2.05A/B/C/D1-169[»]
4WXLX-ray2.33A/B/C/D1-169[»]
ProteinModelPortaliQ4QMV6.
SMRiQ4QMV6.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAX87641; AAX87641; NTHI0725.
KEGGihit:NTHI0725.
PATRICi20181609. VBIHaeInf100748_0674.

Phylogenomic databases

HOGENOMiHOG000243509.
KOiK01462.
OMAiVCIQHEI.
OrthoDBiPOG091H02B0.

Enzyme and pathway databases

BioCyciHINF281310:GJ89-685-MONOMER.

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_HAEI8
AccessioniPrimary (citable) accession number: Q4QMV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: July 19, 2005
Last modified: November 2, 2016
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

3D-structure, Complete 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.